Ginkgo Bioworks DNA Form 10-Q filing Q2 FY2026

PART I—FINANCIAL INFORMATION

Item 1. Financial Statements (Unaudited)

Item 1. Financial Statements.

The accompanying notes are an integral part of these condensed consolidated financial statements.

(1) Includes related party revenue of zero and $420 for the three months ended June 30, 2026 and 2025, respectively, and zero and $8,518 for the six months ended June 30, 2026 and 2025, respectively.

The accompanying notes are an integral part of these condensed consolidated financial statements.

Ginkgo Bioworks Holdings, Inc.

Condensed Consolidated Statements of Stockholders’ Equity

(unaudited)

(in thousands except share data)

The accompanying notes are an integral part of these condensed consolidated financial statements.

Ginkgo Bioworks Holdings, Inc.

Condensed Consolidated Statements of Stockholders’ Equity

(unaudited)

(in thousands except share data)

The accompanying notes are an integral part of these condensed consolidated financial statements.

The accompanying notes are an integral part of these condensed consolidated financial statements.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

1. Basis of Presentation and Summary of Significant Accounting Policies

Business

Ginkgo Bioworks Holdings, Inc.'s (“Ginkgo” or the “Company”) mission is to make biology easier to engineer. Ginkgo sells tools and biological R&D services across a range of industries to government and commercial customers.

Ginkgo offers biological R&D services on our platform and Autonomous Lab to enable our customers to bring their products to market. Historically, Ginkgo’s primary service offering has been cell engineering R&D services (solutions) where Ginkgo performs technical activities. In 2024, Ginkgo expanded its service offerings to include services and lab automation equipment that provide its customers cell engineering tools for biological R&D, where Ginkgo enables its customers to conduct certain in-house R&D activities themselves. Ginkgo’s services and tools are designed to offer customers better results on the dimensions of probability of success, speed, or cost – and ideally on all three.

Our Autonomous Lab is a flexible wet lab built from our Reconfigurable Automation Cart (“RAC”) systems capable of large-scale data generation; it powers generative AI and machine learning (“ML”) tools that enable more successful biological R&D.

Discontinued Operations

On April 3, 2026, the Company completed a divestiture of its Biosecurity business, which was previously reported as a separate segment, whereby Perimeter Systems, Inc. (the “Purchaser” or “Perimeter”) issued to the Company common equity of the Purchaser representing a minority interest in the Purchaser, in exchange for substantially all of the Company’s operations comprising its Biosecurity business (the “Biosecurity Divestiture”). Refer to Note 2 for additional details on the Biosecurity Divestiture.

The Company is presenting the financial results of the Biosecurity business as discontinued operations for all periods presented within the accompanying condensed consolidated statements of operations and cash flows. The accompanying condensed consolidated balance sheet as of December 31, 2025 reflect the transferred Biosecurity assets as held for sale. Prior to the Biosecurity Divestiture, the Biosecurity business provided services to government customers who are working to identify, monitor, prevent, and mitigate biological threats.

Basis of Presentation

The accompanying condensed consolidated financial statements have been prepared in conformity with the rules and regulations of the SEC and generally accepted accounting principles in the United States (“GAAP”) for interim financial reporting. Accordingly, certain detailed disclosures which would normally be included with annual financial statements have been omitted. In the opinion of management, all normal recurring adjustments necessary for a fair presentation have been made. These condensed consolidated financial statements should be read in conjunction with the 2025 Annual Report. Interim results are not necessarily indicative of results for a full year.

Principles of Consolidation

The accompanying condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany accounts and transactions have been eliminated.

Use of Estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, revenues and expenses, and the disclosure of contingent liabilities in the consolidated financial statements. The Company bases its estimates on historical experience and other market-specific or relevant assumptions that it believes to be reasonable under the circumstances. Reported amounts and disclosures reflect the overall economic conditions that management believes are most likely to occur, and the anticipated measures management intends to take. Actual results could differ materially from those estimates. All revisions to accounting estimates are recognized in the period in which the estimates are revised.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

Significant Accounting Policies

There have been no new or material changes to the Company’s significant accounting policies during the six months ended June 30, 2026 as compared to the significant accounting policies described in Note 2 to the Company’s 2025 consolidated financial statements included in the 2025 Annual Report.

Recently Issued Accounting Pronouncements

There were no new recently issued accounting pronouncements that are of significance or potential significance to the Company from those disclosed within Note 2 to the Company’s 2025 consolidated financial statements included in the 2025 Annual Report.

2. Discontinued Operations and Assets Held for Sale

On February 26, 2026, Ginkgo Bioworks, Inc. (the “Seller”), a wholly owned subsidiary of the Company, entered into a Stock Purchase Agreement (the “Purchase Agreement”) with Tower Biosecurity, Inc., also known as Perimeter Systems, Inc. (the “Purchaser” or “Perimeter”), for the Biosecurity Divestiture. The transaction closed on April 3, 2026 (the “Closing Date”). Pursuant to the Purchase Agreement, the Seller contributed to the Purchaser all of the issued and outstanding equity interests of Ginkgo Biosecurity, LLC (“Biosecurity”), constituting substantially all of the Company's operations comprising its Biosecurity business. In exchange, the Purchaser issued to the Seller shares of its common stock representing approximately 20% of the issued and outstanding equity of the Purchaser on a fully diluted basis. The Seller’s common equity interest in the Purchaser constituted approximately 44% of the outstanding common equity of the Purchaser as of the Closing Date.

Concurrently, the Company and Perimeter entered into a Transition Services Agreement (“TSA”) to ensure the continuity of business operations, pursuant to which the Company and Perimeter provide each other specified services on a temporary basis. The Seller provides certain services to the Purchaser, including, but not limited to, information technology access and support, certain scientific services, human resources, finance and accounting functions. The TSA is expected to conclude within 12 months of the Closing Date. The billings under the TSA are not expected to be significant.

The Biosecurity Divestiture represents a strategic shift that has a major effect on the Company's operations and financial results. The Company no longer operates in the biosecurity market since the Closing Date. The Biosecurity Divestiture meets both the criteria to be classified as a discontinued operation. As such, the results of operations of the Biosecurity business are presented as a single line item, “Net income (loss) from discontinued operations, net of tax,”on the condensed consolidated statements of operations for all periods presented. All prior periods presented have been recast accordingly.

Deconsolidation of the Biosecurity business occurred on the Closing Date. In connection with the deconsolidation, the Company recognized a net gain on deconsolidation of $24.5 million (net of the Company's equity interest contributed to Perimeter management) within in the second quarter of 2026. No cash consideration was received by the Company in connection with the Biosecurity Divestiture. The fair value of the retained equity interest in Perimeter of $12.3 million was determined using the Option Pricing Method (“OPM”) under a Black-Scholes framework (a Level 3 fair value measurement), which allocates equity value across Perimeter's capital structure based on the economics of each security class. Volatility was selected based on the historical equity volatility of a set of comparable guideline public companies and a discount for lack of marketability was applied.

Following deconsolidation, the Company accounts for its retained approximately 44% common equity interest in Perimeter using the equity method of accounting. The Company has the ability to exercise significant influence over the operating and financial policies of Perimeter through its common equity ownership and rights under the Stockholders Agreement. The Company will recognize its proportionate share of Perimeter's operation, equaling approximately 44%.

In connection with the Biosecurity Divestiture, approximately 30% of Perimeter's equity was issued to Perimeter management previously employed by Ginkgo. In accordance with ASC 718 and ASC 710, the fair value of the Perimeter equity awarded to Perimeter management (approximately $15.4 million) was recognized as compensation expense in the second quarter of 2026. This amount is presented within discontinued operations on the Company’s condensed consolidated statements of operations. The management compensation tranche was measured at fair value on the Closing Date using the same Option Pricing Method applied to value the Company's common equity interest in Perimeter.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

The following table presents the major components of the “Income (loss) from discontinued operations, net of tax” in the condensed consolidated statements of operations (in thousands):

The following table presents the major components of assets held for sale on the condensed consolidated balance sheet (in thousands):

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

The following table presents the net cash used in discontinued operations in the condensed consolidated statements of cash flows (in thousands):

There were no investing or financing cash flow activities for the discontinued operations in the six months ended June 30, 2026 or 2025, respectively.

The table below provides a reconciliation of the beginning and ending balances for the Company's equity method investment in Perimeter for the six months ended June 30, 2026 (in thousands):

3. Restructuring

In the second quarter of 2024, in connection with the Company’s plans to reduce operational expenditures, management, with the approval of the Company’s Board of Directors, approved and commenced a restructuring plan. This plan included a reduction in labor expenses, primarily through a workforce reduction of more than 50%, and the consolidation and subleasing of certain facilities. Initial workforce reductions commenced in June 2024 and substantially concluded by December 31, 2025. The Company plans to consolidate certain facilities through various actions, including combining office and laboratory operations into fewer locations, subleasing unused or underutilized facilities. While the Company has substantially completed the majority of its facility consolidation actions with excess space available for sublease, the subleasing of unused or underutilized facilities is expected to extend at least throughout 2026 and may not occur prior to termination of such lease, depending on market conditions.

The Company is currently unable to estimate the costs associated with consolidating its facilities. These costs may include, but are not limited to, losses on subleases, contract terminations, asset impairments, sale or disposal of equipment or other long-lived assets, and related costs and fees pertaining to the consolidation, closure, or disposition of facilities. Additional charges may be incurred as the Company progresses its restructuring plan and such charges could be material.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

The following table presents the change in the accrued liability balance related to the restructuring activities, which is included in “Accounts payable” and “Accrued expenses and other current liabilities” in the accompanying condensed consolidated balance sheets (in thousands):

Restructuring charges were zero and $3.6 million during the three months ended June 30, 2026 and 2025, respectively. Restructuring charges were zero and $8.0 million during the six months ended June 30, 2026 and 2025, respectively. Restructuring charges consisted entirely of employee termination costs and other.

4. Fair Value Measurements

The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis (in thousands):

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

(1) The fair value of Synlogic, Inc. warrants is calculated as the quoted price of the underlying common stock, less the unpaid exercise price of the warrants.

Transfers between Levels 1, 2 and 3 are recognized at the end of the reporting period in which a change in valuation technique or methodology occurs. During the six months ended June 30, 2025, transfers into Level 3 consisted of a note receivable that was transferred from Level 2 to Level 3 upon a change in valuation technique. There were no other transfers between Levels 1, 2, or 3 during the six months ended June 30, 2026 or June 30, 2025.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

The table below provides a reconciliation of the beginning and ending balances for assets and liabilities measured at fair value using Level 3 significant unobservable inputs for the six months ended June 30 (in thousands):

Notes Receivable

For all of its notes receivable, the Company has elected the fair value option, under which changes in fair value are recorded in other income (expense), net, in the condensed consolidated statements of operations and comprehensive loss.

The Company holds a senior secured note in the original principal amount of $11.8 million issued by Bolt Threads, Inc. (“Bolt”), which bears interest at 12% per annum, is due December 31, 2027, and is included in other non-current assets at its estimated fair value.

During the six months ended June 30, 2026, Bolt disclosed it ceased operations. Any proceeds recovered from the Bolt note as the result of a potential disposition of Bolt assets are expected to be immaterial. As such, during the six months ended June 30, 2026, the Company reduced the carrying value of the senior secured note to zero.

As of December 31, 2025, the Company used a discounted cash flow model to estimate the fair value of the senior secured note, incorporating significant unobservable inputs such as the recovery rate, a risk-adjusted discount rate, and a potential settlement scenario.

The Company also held a series of convertible debt instruments issued by customers as payment for cell engineering services. The Company used a scenario-based method to value the convertible debt instruments. Under this method, future cash flows are evaluated under various payoff scenarios, probability-weighted, and discounted to present value. The significant unobservable (Level 3) inputs used in the fair value measurement as of December 31, 2025 included scenario probabilities ranging from 5% to 45%, a discount rate of 15.5% and estimated time to event date of approximately one year. Significant changes in these inputs could have resulted in a significantly lower or higher fair value measurement.

As of June 30, 2026, the Company’s convertible notes receivable had an unpaid principal balance of $7.5 million and a fair value of zero, compared to an unpaid principal balance of $9.7 million and a fair value of $0.5 million as of December 31, 2025.

Contingent Consideration

In connection with various business acquisitions, the Company is required to make contingent earnout payments payable upon the achievement of certain technical, commercial and/or performance milestones. The Company also issued restricted stock in connection with acquisitions, which is subject to vesting conditions and is classified as contingent consideration liability.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

The Company may settle a majority of its contingent consideration liabilities in either cash or shares of Class A common stock, at its discretion, with the remainder payable in cash. No contingent consideration liabilities were settled during the six months ended June 30, 2026 or 2025, respectively.

The fair value of contingent consideration related to earnout payments from acquisitions was estimated using unobservable (Level 3) inputs as illustrated in the table below. The fair value of contingent consideration related to restricted stock was estimated using the quoted price of Ginkgo’s Class A common stock, an estimate of the number of shares expected to vest, probability of vesting, and a discount rate. Material increases or decreases in these inputs could result in a higher or lower fair value measurement. Changes in the fair value of contingent consideration are recorded in general and administrative expense in the condensed consolidated statements of operations and comprehensive loss.

The following table provides quantitative information regarding Level 3 inputs used in the fair value measurements of contingent consideration liabilities as of the periods presented:

Nonrecurring Fair Value Measurements

The Company measures the fair value of certain assets, including investments in privately held companies without readily determinable fair values, on a nonrecurring basis when events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable and when observable price changes occur for identical or similar security of the same issuer.

The fair value of non-marketable equity securities is classified within Level 3 in the fair value hierarchy when the Company estimates fair value using unobservable inputs to measure the amount of the impairment loss. The fair value of non-marketable equity securities is classified within Level 2 in the fair value hierarchy when the Company estimates fair value using the observable transaction price paid by third party investors for the identical or similar security of the same issuer.

During the three and six months ended June 30, 2026, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies. During the six months ended June 30, 2025, the Company recorded an impairment of $1.8 million related to an investment in the preferred stock of a privately held company after concluding that the investment had substantially no value. During the three months ended June 30, 2025, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies.

No impairment losses related to Simple Agreements for Future Equity (“SAFEs”) were recorded during the three and six months ended June 30, 2026 or 2025, respectively.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

5. Marketable Securities

Investments in marketable securities, including those classified in cash and cash equivalents, are summarized as follows (in thousands):

The amortized cost and estimated fair value of marketable debt securities at June 30, 2026, including $19.3 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands):

6. Investments and Equity Method Investments

The Company has partnered with other investors to form business ventures, including Motif FoodWorks, Inc. (“Motif”), Allonnia, LLC (“Allonnia”), Arcaea, LLC (“Arcaea”), Verb Biotics, LLC (“Verb Biotics”), BiomEdit, Inc. (“BiomEdit”), and Ayana Bio, LLC (“Ayana Bio”) (collectively “Platform Ventures”). The Company also partners with existing entities, including Genomatica and Synlogic, Inc. (“Synlogic”) (collectively, “Legacy Structured Partnerships”) with complementary assets for synthetic biology applications. The Company holds equity interests in these Platform Ventures and Legacy Structured Partnerships. The Company also holds equity interests in other public and private companies as a result of entering into collaboration and license revenue arrangements with these entities. Refer to Note 2 for additional details on the Company's equity method investment in Perimeter.

The Company accounts for its investments in Platform Ventures under the equity method. Such investments had a carrying value of zero as of June 30, 2026 and December 31, 2025. The Company’s marketable equity securities consist of Synlogic common stock, Synlogic warrants and the shares of common stock of other publicly traded companies. Marketable equity

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

securities are measured at fair value with changes in fair value recorded in other income (expense) in the condensed consolidated statements of operations and comprehensive loss. The Company’s non-marketable equity securities consist of preferred stock of Genomatica and preferred and common stock of other privately held companies without readily determinable fair values. Non-marketable equity securities are initially recorded using the measurement alternative at cost and subsequently adjusted for any impairment and observable price changes in orderly transactions for the identical or a similar security of the same issuer. Impairment losses and adjustments from observable price changes are recorded in loss on investments in the condensed consolidated statements of operations and comprehensive loss.

The Company also holds investments in early-stage synthetic biology product companies via SAFEs. The Company entered into SAFEs in conjunction with a revenue contract with a customer under which the Company grants the customer a prepaid cell engineering services credit equal to the principal amount of the SAFE (the “Purchase Amount”), which may be used and drawn down as payment for the Company’s research and development services. The SAFEs will automatically convert into shares of preferred stock equal to the Purchase Amount divided by the discount price, which is calculated as the price per share sold in a qualified equity financing multiplied by a discount rate. The SAFEs also provide the Company with the right to future equity of the entity in a liquidation scenario or the cash-out amount in liquidation and dissolution scenarios or at the election of the SAFE issuer prior to an agreed outside date. The Company initially records SAFEs at fair value (see Note 4) and adjusts the carrying amount of the instrument at each reporting period for any impairments.

Investments consisted of the following (in thousands):

The components of gain (loss) on investments for each period were as follows (in thousands):

The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of June 30, 2026, including cumulative unrealized losses, were as follows (in thousands):

7. Variable Interest Entities

With respect to the Company’s investments in Perimeter, Motif, Allonnia, Genomatica, Arcaea, BiomEdit, Verb Biotics, and Ayana Bio, the Company has concluded these entities represent variable interest entities (such entities, the “VIEs”).

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

While the Company has board representation on certain of these entities and is involved in the ongoing development activities of these entities via its participation on such entities’ joint steering committees (“JSC”), the Company has concluded that it is not the primary beneficiary of these entities because: (i) the Company does not control the board of directors of any of the VIEs, and no voting or consent agreements exist between the Company and other members of each respective board of directors or other investors, (ii) the holders of preferred security interests in the VIEs hold certain rights that require their consent prior to taking certain actions, which include certain significant operating and financing decisions, and (iii) the Company’s representation on the JSC of each respective entity does not give it control over the development activities of any of the VIEs, as all JSC decisions are made by consensus and there are no agreements in place that would require any of the entities to vote in alignment with the Company. As the Company’s involvement in the VIEs does not give it the power to control the decisions with respect to their development or other activities, which are their most significant activities, the Company has concluded that it is not the primary beneficiary of the VIEs.

Additionally, the Company holds equity interests in certain privately-held companies that are not consolidated as the Company is not the primary beneficiary. As of June 30, 2026 and December 31, 2025, the maximum risk of loss related to the VIEs was limited to the carrying value of its investments in such entities.

Refer to Note 6 for additional details on the Company’s investments and equity method investments.

8. Supplemental Financial Information

Cash, Cash Equivalents and Restricted Cash

The reconciliation of cash, cash equivalents and restricted cash reported within the condensed consolidated balance sheet to the totals shown within the condensed consolidated statements of cash flows is as follows (in thousands):

(1) Includes primarily cash balances collateralizing letters of credit associated with the Company’s facility leases and customer prepayments requiring segregation and restrictions in its use in accordance with the customer agreement.

(2) Includes primarily cash equivalents balances as of June 30, 2026 associated with a customer surety bond to fulfill its obligations under a contract with a U.S. Government National Laboratory and customer prepayments requiring segregation and restrictions in its use in accordance with the customer agreement.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

Supplemental cash flow information

The following table presents non-cash investing and financing activities (in thousands):

Property, Plant and Equipment, net

Property, plant and equipment, net consisted of the following (in thousands):

Capitalization

The following table presents the Company’s authorized, issued, and outstanding common stock as of the dates indicated:

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

At-The-Market Program

On September 4, 2025, the Company entered into a Sales Agreement (the “Sales Agreement”) with Allen & Company LLC (“Allen”), who is acting as the sales agent (the “Agent”), pursuant to which the Company may sell shares of its Class A common stock from time to time at prices and on terms determined by market conditions at the time of offering, up to an aggregate offering price of $100.0 million through or directly to the Agent in one or more at-the-market (“ATM”) offerings. Since inception of the Sales Agreement through June 30, 2026, the Company has issued 3.7 million shares of Class A common stock under the Sales Agreement for net proceeds of $34.6 million.

9. Intangible Assets, net

Intangible assets, net consisted of the following (in thousands):

(1) Gross carrying value and accumulated amortization include the impact of foreign currency translation adjustments.

Amortization expense was $4.1 million and $4.2 million for the three months ended June 30, 2026 and 2025, respectively, and $8.3 million and $8.4 million for the six months ended June 30, 2026 and 2025, respectively. As of June 30, 2026, estimated future amortization expense for identifiable intangible assets is as follows (in thousands):

10. Commitments and Contingencies

Legal Proceedings

From time to time, the Company may in the ordinary course of business be named as a defendant in lawsuits, indemnity claims and other legal proceedings. The Company accrues for a loss contingency when it concludes that the likelihood of a loss is probable and the amount of loss can be reasonably estimated. The Company adjusts its accruals from time to time as it receives additional information. The Company does not believe any pending litigation to be material, or that the outcome of any such pending litigation, in management’s judgment based on information currently available, would have a material adverse effect on the Company’s results of operations, cash flows or financial condition.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

11. Stock-Based Compensation

The following table summarizes stock-based compensation expense by financial statement line item in the Company’s condensed consolidated statements of operations and comprehensive loss for the periods presented (in thousands):

The Company grants stock-based incentive awards pursuant to the 2021 Incentive Award Plan (the “2021 Plan”) and the 2022 Inducement Plan (the “2022 Inducement Plan”). As of June 30, 2026, there were 4,304,034 shares and 298,803 shares available for future issuance under the 2021 Plan and the 2022 Inducement Plan, respectively.

Restricted Stock Units

Restricted stock unit (“RSU”) awards granted before 2025 generally had a four-year requisite service period, with 25% of the shares vesting on the first anniversary of the grant date and the remainder vesting monthly thereafter. RSU awards granted in March 2026 and after will vest in equal quarterly installments through January 2027.

A summary of the RSU activity for the six months ended June 30, 2026 is presented below:

The weighted average grant date fair value of RSUs granted during the six months ended June 30, 2026 and June 30, 2025 was $7.20 and $7.95, respectively.

As of June 30, 2026, there was $27.6 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 1.4 years.

Performance-based Restricted Stock Units

In March 2025, the compensation committee of the Company's Board of Directors approved a grant of performance-based restricted stock unit (“PSU”) awards under the 2021 Plan to substantially all employees. The PSUs were eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2025 cash flow and bookings targets. PSU achievement percentages ranged from 49% to 100% of the award. The grant-date fair value of the PSUs was determined based on the closing price of the Company’s Class A common stock on the grant date.

In March 2026, the compensation committee of the Company's Board of Directors approved a grant of PSU awards under the 2021 Plan to substantially all employees. The PSUs are eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2026 cash flow and bookings targets. Recipients must remain employed through the date the applicable vested shares are distributed, which is expected to occur in March 2027. PSU achievement percentages may range from zero to 100% of the award. The grant-date fair value of the PSUs was determined based on the closing price of the Company’s Class A common stock on the grant date.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

A summary of PSU activity for the six months ended June 30, 2026 is presented below:

As of June 30, 2026, there was $15.0 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately 0.8 years, assuming a 100% PSU achievement rate. Actual expense recognized may vary based on the final achievement rate.

12. Revenue Recognition

Disaggregation of Revenue

The following table sets forth the percentage of revenues by industry based on total revenue:

Revenue includes both cash and non-cash consideration. The non-cash consideration primarily consists of equity received from customers as partial or full payment in certain contracts, which is recognized as revenue as services are provided or upon contract termination. The Company did not receive equity as consideration for any customer contracts entered into during the six months ended June 30, 2026 and June 30, 2025, but continues to recognize non-cash revenue from prior contracts. Revenue recognized relating to non-cash consideration was $0.8 million and $1.2 million for the three months ended and June 30, 2026, and 2025 respectively, and $1.3 million and $9.9 million for the six months ended and June 30, 2026, and 2025 respectively.

The Company’s total revenue is primarily generated from customers located in the United States. For the three months ended months ended June 30, 2026 and 2025, U.S. customers accounted for 83% and 79%, respectively. For the six months ended June 30, 2026 and 2025, U.S. customers accounted for 74% and 80%, respectively. For the six months ended June 30, 2026 and 2025, customers from Denmark accounted for 11% and 11%, respectively.

Contract Balances

The Company recognizes a contract asset when the Company transfers goods or services to a customer before the customer pays consideration or before payment is due, excluding any amounts presented as accounts receivable. The Company had no contract asset balances as of June 30, 2026 and December 31, 2025. The Company’s accounts receivable consists of both billed and unbilled amounts. Unbilled receivables arise when revenue is recognized in excess of invoiced amounts and represent the Company’s unconditional right to consideration for goods or services already transferred to the customer. The

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

balance of unbilled accounts receivable, included in accounts receivable, net in the accompanying condensed consolidated balance sheets, was $7.4 million and $14.5 million as of June 30, 2026 and December 31, 2025, respectively.

Contract liabilities, or deferred revenue, primarily consist of payments received in advance of performance under the contract or when the Company has an unconditional right to consideration under the terms of the contract before it transfers goods or services to the customer. The Company’s collaborative arrangements with its investees and related parties typically include upfront payments consisting of cash or non-cash consideration for future research and development services and non-cash consideration in the form of convertible financial instruments and equity securities for licenses that will be transferred in the future. The Company records the upfront cash payments and fair value of the convertible financial instruments and equity securities as deferred revenue.

The Company also invoices customers based on contractual billing schedules, which results in the recording of deferred revenue to the extent payment is received prior to the Company’s performance of the related services. Contract liabilities are recognized as revenue as (or when) the Company performs under the contract.

During the six months ended June 30, 2026, the Company recognized $13.4 million of revenue that was included in the contract liabilities balance of $94.1 million as of December 31, 2025. During the six months ended June 30, 2025, the Company recognized $35.6 million of revenue that was included in the contract liabilities balance of $126.5 million as of December 31, 2024.

Performance Obligations

The aggregate amount of the transaction price that was allocated to performance obligations that have not yet been satisfied or are partially satisfied as of June 30, 2026 and December 31, 2025 was $113.0 million and $136.8 million, respectively. The Company has elected the practical expedient not to provide the remaining performance obligation disclosures related to contracts for which the Company recognizes revenue on a cost-plus basis in the amount to which it has the right to invoice. As of June 30, 2026, approximately $8.9 million of the unsatisfied or partially satisfied performance obligations is expected to be recognized as revenue in 2026, based on the projected customer program end dates; $35.2 million between 2026 and 2027; $61.6 million between 2026 and 2028; $3.4 million between 2026 and 2029; and $3.9 million between 2026 and 2030.

13. Segment Information

As a result of the Biosecurity Divestiture (Note 2), the Company manages its operations as a single operating and reportable segment. This structure reflects the Company’s internal management framework and the approach its Chief Operating Decision Maker (“CODM”) uses to evaluate operating results and allocate resources.

The Company’s reportable segment is that for which discrete financial information is available and whose results are regularly provided to the Company’s CODM, consisting of the Chief Executive Officer and the President, for the purpose of allocating resources and assessing financial performance. The CODM evaluates the financial performance of the Company’s segment based on loss from continuing operations before income taxes. The CODM is primarily provided with loss from continuing operations before income taxes on a quarterly basis, as well as during the annual budgeting and forecasting process, and uses this information to monitor the Company’s performance, including budget-to-actual results, and to make decisions about the allocation of operating and capital resources. The Company has determined its significant segment expenses are cost of revenue, research and development expenses, and general and administrative expenses (exclusive of certain costs and expenses), which are regularly provided to the CODM.

The CODM is not provided with asset information; therefore, such information is not presented. The accounting policies used to prepare the reportable segments financial information are the same as those used to prepare the Company’s consolidated financial statements. The classification of costs differs from the presentation in the condensed consolidated statement of operations as described below.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

The following table presents summary results of the Company’s reportable segment, including significant expenses, and a reconciliation to loss from continuing operations before income taxes (in thousands):

(1) The costs and operating expenses exclude expenses which are separately captioned below.

(2) Includes $0.4 million and $0.2 million in employer payroll taxes for three months ended June 30, 2026 and 2025, respectively, and $1.3 million and $0.5 million for six months ended June 30, 2026 and 2025, respectively.

(3) See Note 3, Restructuring, for composition of costs.

(4) The carrying cost of excess space includes base rent, common area maintenance charges, and real estate taxes associated with facilities the Company is not occupying, net of any sublease income from these spaces.

(5) Represents transaction and integration costs directly related to mergers, acquisitions, and divestitures, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) securities litigation costs.

(6) Includes interest income, interest expense, loss on investments, changes in fair value of certain assets and liabilities, and other gains and losses.

14. Net Loss per Share

The following potential common shares, presented based on amounts outstanding at each period end, were excluded from the calculation of diluted net loss per share for the periods presented because including them would have been anti-dilutive:

(1) Represents employee and non-employee earnout shares for which the service-based and/or market-based vesting conditions have not been satisfied.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

15. Related Parties

The Company’s significant transactions with its related parties are primarily comprised of revenue generating activities under collaboration and license agreements.

Significant related party transactions included in the condensed consolidated balance sheet, excluding the Company’s investments and equity method investments, are summarized below (in thousands):

Significant related party transactions included in the condensed consolidated statements of operations and comprehensive loss, excluding the losses on the Company’s investments and equity method investments, are summarized below (in thousands):

During the three and six months ended June 30, 2026, the Company recognized zero revenue from related parties.

Refer to Note 6 for additional details on the Company’s investments and equity method investments held in its related parties.

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations.

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with the unaudited condensed consolidated financial statements and related notes thereto included elsewhere in this Quarterly Report on Form 10-Q. This discussion contains forward-looking statements that reflect our plans, estimates and beliefs that involve risks and uncertainties. Actual results may differ materially from those anticipated in these forward-looking statements as a result of many factors, including those discussed in Item 1A “Risk Factors” and “Cautionary Note Regarding Forward-Looking Statements” elsewhere in this Quarterly Report on Form 10-Q and in our 2025 Annual Report.

Overview

Our mission is to make biology easier to engineer.

Ginkgo currently sells cell engineering biological R&D services and tools to government and commercial customers across a range of industries.

Cell Engineering

Ginkgo offers biological R&D services on our platform to enable our customers to bring their products to market. Historically, Ginkgo’s primary service offering has been cell engineering R&D services (solutions) where Ginkgo performs technical activities. In 2024, Ginkgo expanded its service offering to include services that provide our customers cell engineering tools for biological R&D, where Ginkgo enables its customers to conduct certain in-house R&D activities themselves. Our services are designed to offer customers better results on the dimensions of probability of success, speed, or cost – and ideally on all three.

The fundamental advantage of our cell engineering platform over traditional cell engineering done by hand at our customers’ labs is that our platform improves with scale while in-house cell engineering in our customers' labs largely does not. Compounding and mutually reinforcing improvements of our laboratory automation and software infrastructure—our Autonomous Lab—and our reusable data assets enable us to improve our services with each successive project.

Our Autonomous Lab is a flexible wet lab built from our RAC systems capable of large scale data generation; it powers generative AI and ML tools that enable more successful biological R&D. We now offer services providing such data generation, AI and automation tools directly to Ginkgo customers. Our data assets comprise best practices for cell engineering, along with sequences and host cells that have been honed through dozens of programs and can be directly reusable for our cell engineering solutions. We now offer licenses to our host cells and other intellectual property assets, such as our broad metagenomic library.

Cell engineering tools offerings

We charge customers fees for the services we provide in our cell engineering tools offerings. Fees for our automation solutions (RAC systems) are typically earned over a period that covers design, build, and deployment and range from six to twelve months. In addition, we offer support services for our RAC systems with fixed fees covering the support periods.

Fees for our Datapoints services are typically earned over a shorter period of time (weeks to months) than for cell engineering solutions, which may be multi-year programs. A typical deliverable for a Datapoints program is a data package. Fees for cell engineering solutions programs are typically structured as a fixed fee for a fixed scope of work.

Cell engineering solutions

Our cell engineering solutions are typically scoped and delivered as a program ranging in duration from several months to several years. A typical deliverable for the program would comprise an enzyme sequence, or an engineered strain or cell line and its associated bioprocess. For each of these programs, we generate economic value in two primary ways.

First, we charge service fees for Autonomous Lab services, in much the same way that cloud computing companies charge usage fees for utilization of computing capacity or CROs charge for services. R&D is inherently risky and our customers recognize that this is a cost they will incur regardless of success and whether they are working on the program in-house or with a partner. Typically, service fees for a program include a fixed fee for a fixed scope of work and may also include payments contingent upon hitting certain technical milestones. If we are able to deliver program results with less work

through the use of Codebase assets and/or generative AI tools, then we can achieve the same revenue with lower cost or in a shorter duration. Service fees provide a strong foundation of revenue that is independent of any commercialization efforts by our partners.

Second, as the key enabling technology for our customers’ products, we have historically negotiated a value share with our customers (in the form of royalties, milestones, and/or equity interests) in order to align our economics with the success of the programs enabled by our platform. Because we typically do not incur material downstream costs (e.g., manufacturing or product development, which our customers manage), these value share payments flow through with minimal incremental costs. We have structured a variety of value sharing mechanisms, including royalties, lump-sum milestones, and equity payments. As Ginkgo has matured, we have shifted our downstream value towards milestone payments and commercial royalties rather than equity. In addition, commencing in the second quarter of 2024, we announced changes in prospective commercial terms, including the removal of downstream value share from certain program types.

This flexible business model allows for more predictable near-term revenue in up-front research fees and technical milestones without sacrificing our ability to create long-term value with asymmetric upside through downstream value share (typically in the form of a royalty stream, milestone, and/or equity share). As we add more programs to the platform over time, we expect downstream value share to contribute income, which could in turn grow our overall margins and cash flow profile for our cell engineering solutions. The realization of potential revenue related to downstream value in the form of potential future milestone payments and royalties and/or equity consideration is dependent upon a number of factors, including our ability to successfully develop engineered cells, bioprocesses, data packages, or other deliverables, and the product development and commercialization success of our customers.

Discontinued Operations

On April 3, 2026, the Company completed a divestiture of its Biosecurity business, which was previously reported as a separate segment, whereby the Purchaser issued to the Company shares of common equity of the Purchaser representing a minority interest in the Purchaser in exchange for substantially all of the Company’s operations comprising its Biosecurity business (see Note 2 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for further details).

The Company is presenting the financial results for the former Biosecurity business within discontinued operations for all periods presented within its accompanying condensed consolidated statements of operations and cash flows and the accompanying condensed consolidated balance sheet as of December 31, 2025 reflect the transferred Biosecurity assets as held for sale. Prior to the Biosecurity Divestiture, the Biosecurity business provided services to government customers working to identify, monitor, prevent and mitigate biological threats.

Components of Results of Operations

Revenue

We generate revenue primarily through service and license agreements for our tools and solutions offerings. Under our automation solutions agreements we typically provide services related to the design, build, and deployment of our RAC systems as well as ongoing support services. Datapoints agreements typically include fixed fees for services related to producing a data package for our customers and are earned over a shorter time period than legacy cell engineering solutions projects. Under our solutions agreements, we typically provide R&D services for cell programming with the goal of producing an engineered cell that meets a mutually agreed specification. Our customers obtain license rights to the output of our services, which are primarily the optimized strains or cell lines, in order to manufacture and commercialize products derived from that licensed strain or cell line. Generally, the terms of these agreements provide that we receive some combination of: (1) service fees in the form of (i) upfront payments upon consummation of the agreement or other fixed payments, (ii) reimbursement for costs incurred for R&D services and (iii) milestone payments upon the achievement of specified technical criteria, plus (2) downstream value share payments in the form of (i) milestone payments upon the achievement of specified commercial criteria, (ii) royalties on sales of products from or comprising engineered organisms arising from the collaboration or licensing agreement and/or (iii) royalties related to cost of goods sold reductions realized by our customers. Royalties did not comprise a material amount of our revenue during any of the periods presented.

Revenue has historically included transactions with Platform Ventures and Legacy Structured Partnerships where we received non-cash consideration in the form of equity interests and financial instruments that are convertible into equity upon a triggering event. We view the upfront non-cash consideration as prepayments for licenses which will be granted in the future as we complete mutually agreed upon technical development plans. In these instances, we also receive cash consideration for the R&D services performed by us on a fixed fee or cost-plus basis. We are not compensated through

additional milestone or royalty payments under these arrangements. As we perform R&D services under the mutually agreed upon development plans, we recognize a reduction in the prefunded obligation on a cost-plus basis. In some cases we issued the customer a prepaid cell engineering services credit in exchange for the upfront non-cash consideration, which can and has been drawn down as payment for R&D services performed under mutually agreed upon development plans. These arrangements are further described in Notes 6, 7, and 15 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q.

Downstream value share in the form of equity interest appreciation is not recognized as revenue but is expected to contribute to future cash flows upon liquidation, the amount and timing of which is inherently unpredictable. The initial fair market value of the equity interests received may also decrease after contract inception and the amount of cash proceeds eventually realized may be less than the revenue recognized. Equity investments are accounted for under the equity method, cost method or are carried at fair value.

As Ginkgo has matured, we have shifted our downstream value towards milestone payments and commercial royalties rather than equity. In addition, commencing in the second quarter of 2024, we announced changes in prospective commercial terms, including the removal of downstream value share from certain program types.

Costs and Operating Expenses

Cost of Other Revenue

Cost of other revenue consists of costs related to our cell engineering tools offerings, including Datapoints and lab automation solutions. Such costs primarily include hardware, software, materials and labor. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.

Research and Development Expenses

The nature of our business, and primary focus of our activities, generates a significant amount of R&D expenses. R&D expenses represent costs incurred by us for the following:

• development, operation, expansion and enhancement of our Foundry and Codebase; and
• costs incurred to deliver our end-to-end cell engineering solutions offering to customers.

The activities above incur the following expenses:

• personnel compensation and benefits;
• rent, facilities, depreciation, software, professional fees and other direct and allocated overhead expenses; and
• laboratory supplies, consumables and related services provided under agreements with third parties and in-licensing arrangements.

We expense R&D costs as incurred. Our R&D expenses were lower in the first half of 2026 compared to the first half of 2025, primarily due to our restructuring plan announced and commenced in the second quarter of 2024 as we rationalized our current development programs and prioritize our investments in our tools offerings. We expect that our R&D expenses will either remain consistent or decline in 2026 as compared to 2025, reflecting the stabilization of our operational overhead and the impact of our restructuring actions. However, our R&D expenses could increase in 2026 due to continued investment in our tools offerings. The nature, timing, and estimated costs required to support our growth will be dependent on advances in technology, our ability to attract new customers, and the rate of market penetration within our existing customer industries.

General and Administrative Expenses

G&A expenses consist primarily of costs for personnel in executive, business development, finance, human resources, legal and other corporate administrative functions. G&A expenses also include professional legal services fees and costs incurred relating to litigation, corporate, intellectual property and patent matters, professional fees incurred for accounting, auditing, tax and administrative consulting services, insurance costs, and facility-related costs not otherwise included in R&D expenses.

Our G&A expenses were lower in the first half of 2026 compared to the first half of 2025, primarily due to our restructuring plan announced and commenced in the second quarter of 2024, as we reduced our operational overhead. We expect that our G&A expenses will either remain consistent or decline in 2026 as compared to 2025, reflecting the stabilization of our operational overhead and the impact of our restructuring actions. However, our G&A expenses could

increase in 2026 due to employee incentive programs offered. Conversely, we intend to maintain a strategic and opportunistic approach regarding inorganic G&A expenses arising from mergers, acquisitions, divestitures, and other inorganic growth initiatives.

Restructuring Charges

Restructuring charges are related to our restructuring plan, which was announced and commenced in the second quarter of 2024 and substantially concluded in the fourth quarter of 2025. These charges primarily included severance and other employee termination costs from a reduction in force that commenced in 2024, as well as the impairment of a right-of-use asset due to the subleasing of a facility as part of real estate consolidation. While the Company has substantially completed the majority of its facility consolidation actions with excess space available for sublease, the subleasing of unused or underutilized facilities is expected to extend throughout 2026 and may not occur prior to termination of such lease, depending on market conditions.

Additional details are included in Note 3, Restructuring, of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q.

Interest Income, Net

Interest income, net consists primarily of interest earned on our cash and cash equivalents and marketable debt securities.

Loss on Equity Method Investment

Loss on equity method investments includes our share of losses from our equity method investment in Perimeter Systems, Inc.

Gain (Loss) on Investments

Gain (Loss) on investments includes the change in fair value of our marketable equity securities in publicly traded companies and impairment losses recognized on non-marketable equity securities in privately held companies.

Other Income (Expense), Net

Other income (expense), net primarily consists of changes in the fair value of notes receivable that we elected to account for under the fair value option.

Provision for Income Taxes

Income taxes are recorded in accordance with ASC 740, Income Taxes, which provides for deferred taxes using an asset and liability approach. We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in our financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the financial statement and tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. A valuation allowance against deferred tax assets is recorded if, based on the weight of the available evidence, it is more likely than not that some or all the deferred tax assets will not be realized. For all periods presented, we have recorded a valuation allowance against the deferred tax assets that are not expected to be realized.

We account for uncertain tax positions using a more-likely-than-not threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors, including, but not limited to, changes in the law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position.

Income taxes are determined at the applicable tax rates adjusted for non-deductible expenses, R&D tax credits and other permanent differences. Our income tax provision may be affected by changes to our estimates.

Results of Operations

Comparison of the Three and Six Months Ended June 30, 2026 and 2025

The following table presents our results of continuing operations for the periods indicated:

Revenue

Revenue was $20.2 million for the three months ended June 30, 2026, compared to $39.1 million for the three months ended June 30, 2025, a decrease of $19.0 million. This decrease was primarily due to a decrease in the scope of services provided to a large enterprise customer in the agriculture industry and decrease in programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries.

Revenue was $39.6 million for the six months ended June 30, 2026, compared to $77.4 million for the six months ended June 30, 2025, a decrease of $37.7 million. This decrease was primarily due to the recognition of $7.5 million in non-cash revenue from the release of a deferred revenue balance associated with the terminated BiomEdit, Inc. contract in the first quarter of 2025, a decrease in the scope of services provided to a large enterprise customer in the agriculture industry, and decrease in programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries.

As discussed above in Components of Results of Operations, Cell Engineering revenue comprises both cash and non-cash consideration. Revenue recognized relating to non-cash consideration decreased from $1.2 million for the three months ended June 30, 2025 to $0.8 million for the three months ended June 30, 2026, and from $9.9 million for the six months ended June 30, 2025 to $1.3 million for the six months ended June 30, 2026, primarily due to lower non-cash revenue from other customers, and the recognition of $7.5 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated BiomEdit contract in the first quarter of 2025.

Cost of Other Revenue

The cost of other revenue was $1.7 million for the three months ended June 30, 2026, compared to $5.4 million for the three months ended June 30, 2025, a decrease of $3.7 million. This decrease was primarily due to reductions in direct equipment expenses incurred for lab automation solutions customers.

The cost of other revenue was $4.8 million for the six months ended June 30, 2026, compared to $9.5 million for the six months ended June 30, 2025, a decrease of $4.7 million. This decrease was primarily due to reductions in direct equipment expenses incurred for lab automation solutions customers.

Research and Development Expenses

Our research and development expenses principally relate to the development of new offerings and the operation, expansion and enhancement of our existing service offerings utilizing our proprietary platform to our cell engineering customers. Research personnel costs, including stock-based compensation, is our largest expense, totaling $17.9 million and $23.7 million for the three months ended June 30, 2026 and June 30, 2025, respectively and $41.5 million and $54.4 million for the six months ended June 30, 2026 and June 30, 2025, respectively. Our remaining research and development costs are comprised primarily of rent and related facilities costs, information technology costs, depreciation pertaining to facilities and equipment, laboratory consumables, contract services, and routine costs and fees.

Research and development expenses were $46.2 million for the three months ended June 30, 2026, compared to $53.4 million for the three months ended June 30, 2025, a decrease of $7.2 million. This decrease was primarily driven by reductions of $4.8 million in stock-based compensation expense (inclusive of employer payroll taxes), $4.4 million in personnel-related compensation and benefits expenses, and $3.0 million in depreciation and amortization. These decreases were partially offset by an increase of $4.3 million in allocated overhead expenses and $0.7 million in other operating expenses.

Research and development expenses were $96.1 million for the six months ended June 30, 2026, compared to $124.3 million for the six months ended June 30, 2025, a decrease of $28.2 million. This decrease was primarily driven by reductions of $13.7 million in personnel-related compensation and benefits expenses, $9.8 million outside services, $5.9 million in stock-based compensation expense (inclusive of employer payroll taxes), $4.9 million in depreciation and amortization, and $0.2 million in other operating expenses. These decreases were partially offset by an increase of $6.3 million in allocated overhead expenses.

General and Administrative Expenses

General and administrative expenses were $30.8 million for the three months ended June 30, 2026, compared to $35.0 million for the three months ended June 30, 2025, a decrease of $4.2 million. This decrease was primarily driven by reductions of $6.2 million in stock-based compensation expense (inclusive of employer payroll taxes) and $3.1 million in personnel-related compensation and benefits expenses. These decreases were partially offset by increases of $2.9 million in earnout remeasurement, $2.0 million in rent and facilities expenses, and $0.2 million in other operating expenses.

General and administrative expenses were $68.6 million for the six months ended June 30, 2026, compared to $74.7 million for the six months ended June 30, 2025, a decrease of $6.1 million. This decrease was primarily driven by reductions of $8.9 million in personnel-related compensation and benefits expenses, $6.1 million in stock-based compensation expense (inclusive of employer payroll taxes), and $1.1 million in other operating expenses. These decreases were partially offset by increases of $5.8 million in rent and facilities expenses and $4.2 million in earnout remeasurement.

Restructuring Charges

Restructuring charges were zero and $3.6 million for the three months ended June 30, 2026 and June 30, 2025, respectively, and zero and $8.0 million for the six months ended June 30, 2026 and June 30, 2025, respectively. Restructuring charges relate to our restructuring plan, which was announced and commenced in the second quarter of 2024 and substantially concluded in the fourth quarter of 2025. These charges primarily consisted of employee termination costs

from the reduction in force. See Note 3 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for further details.

Interest Income, Net

Interest income, net was $3.2 million for the three months ended June 30, 2026, compared to $6.1 million for the three months ended June 30, 2025, a decrease of $2.9 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Interest income, net was $6.8 million for the six months ended June 30, 2026, compared to $12.2 million for the six months ended June 30, 2025, a decrease of $5.3 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Loss on Equity Method Investment

Loss on equity method investment includes our share of losses from our equity method investment in Perimeter Systems, Inc.

Gain (Loss) on Investments

Gain on investments was $2.0 million and a loss of $0.2 million for the three months ended June 30, 2026 and June 30, 2025, respectively. The change was primarily driven by gains on our marketable equity investments in the second quarter of 2026.

Gain on investments was $0.8 million and a loss of $3.9 million for the six months ended June 30, 2026 and June 30, 2025, respectively. The change was primarily driven by gains on our marketable equity investments in the second quarter of 2026 and higher impairment losses on our non-marketable equity investments in privately held companies in 2025. We assess our non-marketable equity investments quarterly for potential impairment and remeasure them to fair value when events or changes in circumstances indicate that their carrying value may not be recoverable.

Other Income (Expense), Net

We recorded net other income of $0.8 million for the three months ended June 30, 2026, compared to net other expense of $1.2 million for the three months ended June 30, 2025, a decrease of $2.0 million. This increase was primarily due to increased sales of excess equipment.

We recorded net other expense of $6.3 million for the six months ended June 30, 2026, compared to net other expense of $5.8 million for the six months ended June 30, 2025, a decrease of $0.5 million. This increase was primarily due to losses on the change in fair value of a note receivable accounted for under the fair value option recorded in 2026 and 2025.

Non-GAAP Information

In addition to our results determined in accordance with GAAP, we use earnings before interest, taxes, depreciation and amortization (“EBITDA”) and Adjusted EBITDA internally to evaluate our performance and make financial and operational decisions. We believe these non-GAAP measures, when viewed with our GAAP results, may be helpful to investors in assessing our operating performance.

We define EBITDA as net loss from continuing operations attributable to Ginkgo Bioworks Holdings, Inc. stockholders before the impact of interest income, interest expense, provision for income taxes and depreciation and amortization.

We define Adjusted EBITDA as EBITDA adjusted for stock-based compensation expense, gain or loss on equity method investments, gain or loss on investments, change in fair value of warrant liabilities, gain or loss on deconsolidation of subsidiaries, transaction and integration costs associated with planned, completed or terminated mergers, acquisitions, and divestitures, including related litigation costs, restructuring and impairment charges (inclusive of impairments of goodwill and long-lived assets), and certain other income and expenses. We believe that the use of EBITDA and Adjusted EBITDA provides an additional tool for investors to use in evaluating ongoing operating results and trends because it eliminates the effect of financing activities, investing activities, and certain non-cash charges and other items that are not related to our core operating performance or affect comparability period over period.

Our non-GAAP financial measures have limitations as analytical tools and should not be considered in isolation or as a substitute for GAAP performance measures. These measures exclude significant expenses and income required by GAAP, which impacts their alignment with consolidated financial statements. They also rely on management’s judgment to

determine which items are included or excluded, making them inherently subjective. Additionally, non-GAAP measures lack uniform definitions and may differ from those used by other companies, limiting comparability. A reconciliation of EBITDA and Adjusted EBITDA to net loss from continuing operations, the most directly comparable GAAP financial measure, is presented below:

(1) All periods include non-cash revenue when earned, including $7.5 million recognized in the six months ended March 31, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement.

(2) Includes $0.4 million and $0.2 million in employer payroll taxes for the three months ended June 30, 2026 and 2025, respectively. Includes $1.3 million and $0.5 million in employer payroll taxes for the six months ended June 30, 2026 and 2025, respectively.

(3) Restructuring charges primarily consist of employee termination costs from the reduction in force commenced in June 2024.

(4) Represents transaction and integration costs directly related to mergers, acquisitions, and divestitures, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) securities litigation costs. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero for both the three and six months ended June 30, 2026 and June 30, 2025, respectively.

Liquidity and Capital Resources

Sources of Liquidity

As of June 30, 2026, we had cash and cash equivalents and marketable securities of $302.2 million, which we believe will be sufficient to enable us to fund our projected operations through at least the next 12 months from the date of filing of this Quarterly Report on Form 10-Q.

At-The-Market Program

On August 7, 2025, we filed a universal shelf registration statement on Form S-3, which was declared effective by the SEC on August 14, 2025, on which we registered for sale up to $500 million of any combination of our Class A common stock, preferred stock, warrants, and/or units from time to time and at prices and on terms that we may determine. On September 4, 2025, the Company entered into the Sales Agreement with Allen, who is acting as the Agent, pursuant to which the Company may sell shares of its Class A common stock from time to time at prices and on terms determined by market conditions at the time of offering, up to an aggregate offering price of $100.0 million through or directly to the Agent in one or more ATM offerings. Since inception of the Sales Agreement through June 30, 2026, the Company has issued 3.7 million shares of Class A common stock under the Sales Agreement for net proceeds of $34.6 million. We currently intend

to use the net proceeds from this offering for general corporate purposes, which may include, but are not limited to, financing our operations, technology development, working capital and capital expenditures.

Material Cash Requirements

We anticipate that our expenditures will exceed our revenue through at least the next 12 months from the date of filing of this Quarterly Report on Form 10-Q, as we:

• continue our R&D activities under existing and new programs and further invest in and expand our tools offerings;
• upgrade, expand or adapt our operational, financial and management systems and support our operations;
• potentially acquire and integrate companies, assets or intellectual property that advance our company objectives; and
• maintain, expand, and protect our intellectual property.

Surety Bond

In April 2026, the Company was required to restrict $47.0 million of cash and cash equivalents to secure a surety bond of the same amount to fulfill its obligations under a contract with a U.S. Government National Laboratory related to the sale of RAC automation equipment. The $47.0 million will remain restricted until the Company completes all of its obligations under the contract. Currently the Company expects the cash to be restricted until 2029.

Cash Flows

The following table provides information regarding our cash flows for each period presented:

Operating Activities - Continuing Operations

Net cash used in operating activities for the six months ended June 30, 2026 consisted of a net loss from continuing operations of $133.4 million, adjusted for net change in operating assets and liabilities of $27.3 million and non-cash charges of $72.1 million. The net change in operating assets and liabilities was primarily due to (i) a $10.7 million decrease in operating lease liabilities from rent payments, (ii) a $7.7 million decrease in accounts payable, accrued expenses and other current liabilities primarily due to a payment associated with a minimum purchase obligation, (iii) a $6.1 million decrease in other non-current liabilities primarily due to a payment associated with a minimum purchase obligation, (iv) a $5.6 million decrease in deferred revenue primarily from the recognition of previously deferred revenue, partially offset by (v) a $3.5 million decrease in accounts receivable due to timing of customer billings. Non-cash adjustments primarily consisted of $25.1 million of depreciation and amortization, $23.4 million of stock-based compensation expense, $13.3 million non-cash lease expense, a $6.8 million change in fair values of various assets and liabilities, a $4.7 million loss on our equity method investment in Perimeter, and a $0.8 million gain on investments.

Net cash used in operating activities for the six months ended June 30, 2025 consisted of a net loss from continuing operations of $136.5 million, adjusted for net change in operating assets and liabilities of $30.9 million and non-cash charges of $86.2 million. The net change in operating assets and liabilities was primarily due to (i) a $24 million decrease in deferred revenue primarily from one-time releases of deferred revenue balances associated with terminated customer contracts and the recognition of previously deferred revenue, (ii) a $11.6 million decrease in operating lease liabilities from rent payments, partially offset by (iii) a $3.8 million decrease in operating lease right-of-use assets from lease incentives received, (iv) a $3.3 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation under a supplier agreement, and (v) a $2.2 million decrease in

accounts receivable due to timing of customer billings. Non-cash adjustments primarily consisted of $36.2 million of stock-based compensation expense, $30.1 million of depreciation and amortization, $14.9 million non-cash lease expense, a $1.1 million change in fair values of various assets and liabilities, and a $4.0 million loss on investments.

Operating Activities - Discontinued Operations

Net cash used in operating activities for the six months ended June 30, 2026 consisted of net income from discontinued operations of $4.1 million, adjusted for net change in operating assets and liabilities of $0.2 million and non-cash charges of $6.6 million. The net change in operating assets and liabilities was primarily due to (i) a $7.8 million decrease in accounts receivable due to collections of customer billings, partially offset by (ii) $8.1 million decrease in accounts payable, accrued expenses and other current liabilities. Non-cash adjustments primarily consisted of a $24.5 million gain on deconsolidation recorded upon the closing of the sale of the Biosecurity business (see Note 2 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q), $17.3 million of stock-based compensation expense, and $0.6 million of depreciation and amortization.

Net cash used in operating activities for the six months ended June 30, 2025 consisted of a net loss from discontinued operations of $14.8 million, adjusted for net change in operating assets and liabilities of $3.3 million and non-cash charges of $7.6 million. The net change in operating assets and liabilities was primarily due to (i) a $2.6 million increase in accounts receivable due to timing of customer billings, (ii) a $1.8 million decrease in accounts payable, accrued expenses and other current liabilities, partially offset by (iii) a $0.8 million decrease in prepaid expenses and other current assets, and (iv) a $0.3 million increase in deferred revenue. Non-cash adjustments primarily consisted of $6.5 million of stock-based compensation expense and $1.1 million of depreciation and amortization.

Investing Activities

Net cash provided by investing activities for the six months ended June 30, 2026 primarily consisted of purchases of marketable debt securities of $127.4 million, maturities of marketable debt securities of $166.2 million, and purchases of property and equipment of $4.6 million primarily related to the build out of our Autonomous Lab.

Net cash used in investing activities for the six months ended June 30, 2025 primarily consisted of purchases of marketable debt securities of $320.1 million, maturities of marketable debt securities of $65.0 million, and purchases of property and equipment of $7.7 million related to the build-out of new office and laboratory space near our headquarters.

Financing Activities

Net cash provided by financing activities for the six months ended June 30, 2026 primarily consisted of $16.5 million in net proceeds from the ATM offering.

Net cash used in financing activities for the six months ended June 30, 2025 primarily consisted of principal payments on finance leases.

Critical Accounting Estimates

There have been no material changes to our critical accounting estimates as compared to the critical accounting estimates disclosed in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our 2025 Annual Report.

Recently Issued Accounting Pronouncements

See Note 1, Basis of Presentation and Summary of Significant Accounting Policies, of our condensed consolidated financial statements contained in Part I, Item 1 of this Quarterly Report on Form 10-Q for a discussion of recently issued accounting pronouncements, as disclosed in our 2025 Annual Report.

Item 3. Quantitative and Qualitative Disclosures About Market Risk.

Interest Rate Risk

We are exposed to interest rate risk on our cash equivalents and marketable debt securities. As of June 30, 2026, we had cash equivalents and marketable debt securities of $303.7 million, consisting of highly liquid investments in money market funds, U.S. Treasury securities, corporate bonds, and commercial paper. We do not enter into investments for trading or speculative purposes. Our investments are exposed to market risk due to fluctuations in interest rates, which may affect our

interest income and the fair market value of our investments. However, due to the short-term nature and quality of investments in our portfolio, an immediate change in market interest rates of 100 basis points would not have a material impact on our consolidated financial statements.

Foreign Currency Exchange Rate Risk

We are subject to foreign currency exchange rate risk from the translation of the financial statements of our foreign subsidiaries, whose financial condition and results of operations are reported in their local currencies and then translated into U.S. dollars at the applicable currency exchange rate for inclusion in our condensed consolidated financial statements. Foreign currency translation gain (loss) was de minimis and $2.6 million for the three months ended June 30, 2026 and 2025, respectively, and $(0.6) million and $3.4 million for the six months ended June 30, 2026 and 2025, respectively. Foreign currency translation adjustments are accounted for as a component of accumulated other comprehensive income within stockholders’ equity. Additionally, we have contracted with and may continue to contract with foreign customers, suppliers, and contractors. We do not believe that an immediate 10% increase or decrease in the relative value of the U.S. dollar to other currencies would have a material effect on operating results or financial condition.

Inflation Risk

Inflation generally affects us by increasing our cost of labor, laboratory supplies, consumables and equipment. We do not believe that inflation had a material effect on our business, financial condition or results of operations during the six months ended June 30, 2026.

Item 4. Controls and Procedures.

Evaluation of Disclosure Controls and Procedures

Our disclosure controls and procedures are designed to ensure that information required to be disclosed in the reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the rules and forms of the SEC, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. The Chief Executive Officer and the Chief Financial Officer, with assistance from other members of management, have reviewed the effectiveness of our disclosure controls and procedures as of June 30, 2026, and, based on their evaluation, have concluded that the disclosure controls and procedures were effective as of such date.

Changes in Internal Control over Financial Reporting

There have been no changes in our internal control over financial reporting (as such term is defined in Exchange Act Rule 13a–15(f) and 15d-15(f)) during the most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II—OTHER INFORMATION

Item 1. Legal Proceedings.

From time to time, the Company may in the ordinary course of business be named as a defendant in lawsuits, indemnity claims and other legal proceedings. The Company does not believe any pending litigation to be material, or that the outcome of any such pending litigation, in management’s judgment based on information currently available, would have a material adverse effect on the Company’s results of operations, cash flows or financial condition.

See Note 10, Commitments and Contingencies, to the unaudited condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q.

Item 1A. Risk Factors.

An investment in our securities involves a high degree of risk. You should carefully consider the risk factors that appear in Part I, Item 1A. “Risk Factors” of our 2025 Annual Report, before making an investment decision. Our business, prospects, financial condition or operating results could decline due to any of these risks and, as a result, you may lose all or part of your investment. There have been no material changes to the risk factors that appear in our 2025 Annual Report.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds.

None.

Item 3. Defaults Upon Senior Securities.

None.

Item 4. Mine Safety Disclosures.

None.

Item 5. Other Information.

None.

Item 6. Exhibits.

*Filed herewith.