Ginkgo Bioworks Holdings, Inc. 10-Q

Item 1. Financial Statements. Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Balance Sheets (unaudited) (in thousands, except share data) As of March 31, 2026 As of December 31, 2025 Assets Current assets: Cash and cash equivalents $ 143,864 $ 167,202 Marketable securities 229,592 255,418 Accounts receivable, net 19,815 24,026 Accounts receivable - related parties 454 229 Prepaid expenses and other current assets 16,230 24,963 Total current assets 409,955 471,838 Property, plant and equipment, net 163,020 167,371 Operating lease right-of-use assets 353,804 360,918 Investments 14,703 15,066 Intangible assets, net 48,860 53,482 Other non-current assets 39,522 47,167 Assets held for sale 3,211 3,854 Total assets $ 1,033,075 $ 1,119,696 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 16,309 $ 10,566 Deferred revenue (includes $ 98 and $ 98 from related parties) 14,910 18,946 Accrued expenses and other current liabilities 48,376 66,458 Total current liabilities 79,595 95,970 Non-current liabilities: Deferred revenue, net of current portion (includes $ 64,810 and $ 64,787 from related parties) 77,895 75,182 Operating lease liabilities, non-current 410,700 417,078 Other non-current liabilities 21,732 22,876 Total liabilities 589,922 611,106 Commitments and contingencies (Note 10) Stockholders’ equity: Preferred stock, $ 0.0001 par value; 200,000,000 shares authorized; none issued — — Common stock, $ 0.0001 par value (Note 8) 6 6 Additional paid-in capital 6,674,860 6,657,053 Accumulated deficit ( 6,232,907 ) ( 6,150,320 ) Accumulated other comprehensive income 1,194 1,851 Total stockholders’ equity 443,153 508,590 Total liabilities and stockholders’ equity $ 1,033,075 $ 1,119,696 The accompanying notes are an integral part of these condensed consolidated financial statements. 1 Table of Contents Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Statements of Operations and Comprehensive Loss (unaudited) (in thousands, except share data) Three Months Ended March 31, 2026 2025 Revenue (1) $ 19,474 $ 38,230 Costs and operating expenses: Cost of other revenue 3,098 4,090 Research and development 49,920 70,923 General and administrative 37,830 39,723 Restructuring charges — 4,466 Total operating expenses 90,848 119,202 Loss from operations ( 71,374 ) ( 80,972 ) Other income (expense): Interest income, net 3,596 6,081 Loss on investments ( 1,214 ) ( 3,693 ) Other expense, net ( 7,147 ) ( 4,638 ) Total other expense ( 4,765 ) ( 2,250 ) Loss from continuing operations before income taxes ( 76,139 ) ( 83,222 ) Income tax (benefit) expense ( 80 ) 88 Net loss from continuing operations $ ( 76,059 ) $ ( 83,310 ) Net loss from discontinued operations, net of tax ( 6,528 ) ( 7,647 ) Net loss $ ( 82,587 ) $ ( 90,957 ) Net loss per share: Basic from continuing operations $ ( 1.28 ) $ ( 1.54 ) Basic from discontinued operations ( 0.11 ) ( 0.14 ) Basic $ ( 1.39 ) $ ( 1.68 ) Weighted average common shares outstanding: Basic 59,563,454 54,241,619 Comprehensive loss: Net loss ( 82,587 ) ( 90,957 ) Other comprehensive (loss) income: Foreign currency translation adjustment ( 579 ) 849 Unrealized gains (loss) on available-for-sale securities ( 78 ) 107 Total other comprehensive (loss) income ( 657 ) 956 Comprehensive loss $ ( 83,244 ) $ ( 90,001 ) (1) Includes related party revenue of zero and $ 8,098 for the three months ended March 31, 2026 and 2025, respectively. The accompanying notes are an integral part of these condensed consolidated financial statements. 2 Table of Contents Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Statements of Stockholders’ Equity (unaudited) (in thousands except share data) Three Months Ended March 31, 2026 Common Stock Shares Amount Additional Paid-In Capital Accumulated Deficit Accumulated Other Comprehensive Income (Loss) Total Stockholders’ Equity Balance as of December 31, 2025 58,207,298 $ 6 $ 6,657,053 $ ( 6,150,320 ) $ 1,851 $ 508,590 Issuance of common stock upon exercise or vesting of equity awards 3,453,490 — — — — — Stock-based compensation expense — — 17,807 — — 17,807 Other comprehensive income — — — — ( 657 ) ( 657 ) Net loss — — — ( 82,587 ) — ( 82,587 ) Balance as of March 31, 2026 61,660,788 $ 6 $ 6,674,860 $ ( 6,232,907 ) $ 1,194 $ 443,153 The accompanying notes are an integral part of these condensed consolidated financial statements. 3 Table of Contents Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Statements of Stockholders’ Equity (unaudited) (in thousands except share data) Three Months Ended March 31, 2025 Common Stock Shares Amount Additional Paid-In Capital Accumulated Deficit Accumulated Other Comprehensive Income (Loss) Total Stockholders’ Equity Balance as of December 31, 2024 54,365,785 $ 5 $ 6,555,416 $ ( 5,837,557 ) $ ( 1,806 ) $ 716,058 Issuance of common stock upon exercise or vesting of equity awards 332,461 — — — — — Release of 18,265 common shares from escrow related to acquisition — — 939 — — 939 Stock-based compensation expense — — 20,431 — — 20,431 Other comprehensive income — — — — 956 956 Net loss — — — ( 90,957 ) — ( 90,957 ) Balance as of March 31, 2025 54,698,246 $ 5 $ 6,576,786 $ ( 5,928,514 ) $ ( 850 ) $ 647,427 The accompanying notes are an integral part of these condensed consolidated financial statements. 4 Table of Contents Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Statements of Cash Flows (unaudited) (in thousands) Three Months Ended March 31, 2026 2025 Cash flows from operating activities: Net loss from continuing operations $ ( 76,059 ) $ ( 83,310 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 12,799 14,822 Stock-based compensation 15,853 17,386 Loss on investments 1,214 3,693 Change in fair value of notes receivable 6,759 5,285 Change in fair value of contingent consideration — ( 1,302 ) Non-cash lease expense 7,114 7,379 Accretion of discount on marketable securities ( 120 ) — Other non-cash activity 185 149 Changes in operating assets and liabilities: Accounts receivable ( 242 ) ( 667 ) Prepaid expenses and other current assets 5,930 ( 581 ) Operating lease right-of-use assets — 3,675 Other non-current assets 94 ( 167 ) Accounts payable, accrued expenses and other current liabilities ( 11,601 ) 8,869 Deferred revenue, current and non-current (includes zero and $( 7,878 ) from related parties) ( 2,606 ) ( 13,190 ) Operating lease liabilities, current and non-current ( 4,995 ) ( 4,790 ) Other non-current liabilities ( 758 ) — Net cash used in operating activities - continuing operations ( 46,433 ) ( 42,749 ) Net cash used in operating activities - discontinued operations ( 253 ) ( 8,772 ) Net cash used in operating activities ( 46,686 ) ( 51,521 ) Cash flows from investing activities: Purchases of marketable debt securities ( 83,161 ) ( 191,182 ) Maturities of marketable debt securities 108,178 — Purchases of property and equipment ( 1,933 ) ( 7,622 ) Other 48 120 Net cash provided by (used in) investing activities 23,132 ( 198,684 ) Cash flows from financing activities: Principal payments on finance leases ( 19 ) ( 207 ) Net cash used in financing activities ( 19 ) ( 207 ) Effect of foreign exchange rates on cash and cash equivalents ( 129 ) 74 Net decrease in cash, cash equivalents and restricted cash ( 23,702 ) ( 250,338 ) Cash and cash equivalents, beginning of period 167,202 561,572 Restricted cash, beginning of period 45,169 44,171 Cash, cash equivalents and restricted cash, beginning of period 212,371 605,743 Cash and cash equivalents, end of period 143,864 312,420 5 Table of Contents Restricted cash, end of period 44,805 42,985 Cash, cash equivalents and restricted cash, end of period $ 188,669 $ 355,405 The accompanying notes are an integral part of these condensed consolidated financial statements. 6 Table of Contents 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 our 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 February 26, 2026, the Company entered into a definitive agreement for the sale of its Biosecurity business, which was previously reported as a separate segment (the “Biosecurity Divestiture”). The Biosecurity Divestiture was completed on April 3, 2026 (the “Closing Date”) whereby, Perimeter Systems, Inc. (the “Purchaser”) 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 Company and the Purchaser also entered into a transition services agreement (the “TSA”) on the Closing Date (Note 2 ). 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 sheets as of March 31, 2026 and 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. 7 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) Significant Accounting Policies Other than as noted below, there have been no new or material changes to the Company’s significant accounting policies during the three months ended March 31, 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 the Purchaser for the sale of its Biosecurity business, which was previously reported as a separate segment. The Biosecurity Divestiture was completed on the Closing Date whereby the Purchaser issued to the Company shares of common equity of the Purchaser representing approximately 20 % of the issued and outstanding equity of the Purchaser on a fully diluted basis. The common equity interest in the Purchaser constituted approximately 44 % of the outstanding common equity of the Purchaser as of the Closing Date. The Biosecurity Divestiture is considered a strategic shift that will have a significant impact on the Company’s operations and financial results. The Company has continuing involvement in the Biosecurity business in the form of the Company’s retained equity interest. Accordingly, certain assets of the Biosecurity business are classified as assets held for sale on the accompanying condensed consolidated balance sheets at March 31, 2026 and December 31 2025. The results of operations for the Biosecurity business have been classified as discontinued operations within the condensed consolidated statements of operations and cash flows for the three months ended March 31, 2026 and 2025. The following table presents the major components of the “Loss from discontinued operations, net of tax” in the condensed consolidated statements of operations (in thousands): Three Months Ended March 31, 2026 2025 Revenue $ 6,210 $ 10,088 Costs and operating expenses: Cost of revenue 5,352 7,957 General and administrative 7,701 9,320 Restructuring charges — 807 Total operating expenses 13,053 18,084 Loss from operations ( 6,843 ) ( 7,996 ) Other income 315 349 Total other income (expense) 315 349 Loss from discontinued operations $ ( 6,528 ) $ ( 7,647 ) 8 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) The following table presents the major components of assets held for sale on the condensed consolidated balance sheets (in thousands): As of March 31, As of December 31, 2026 2025 Intangible assets, net $ 2,910 $ 3,442 Property, plant and equipment, net 301 412 Total assets held for sale $ 3,211 $ 3,854 The following table presents the net cash used in discontinued operations in the condensed consolidated statements of cash flows (in thousands): Three Months Ended March 31, 2026 2025 Cash flows from operating activities: Loss from discontinued operations $ ( 6,528 ) $ ( 7,647 ) Adjustments to reconcile net loss from discontinued operations to net cash used in operating activities - discontinued operations: Depreciation and amortization 561 544 Stock-based compensation 1,954 3,045 Changes in operating assets and liabilities: Accounts receivable 4,242 ( 4,026 ) Prepaid expenses and other current assets 132 1,043 Accounts payable, accrued expenses and other current liabilities ( 1,934 ) ( 2,450 ) Deferred revenue, current and non-current 1,320 719 Net cash used in operating activities - discontinued operations $ ( 253 ) $ ( 8,772 ) There were no investing or financing cash flow activities for the discontinued operations in the three months ended March 31, 2026 or 2025, respectively. The Purchase Agreement includes a TSA between the Seller and the Purchaser. The purpose of this agreement is to ensure the continuity of business operations by having the Seller provide 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 includes fixed and variable payments depending on the services used. Services rendered pursuant to the TSA are expected to conclude within 12 months. The billings under the TSA are not expected to be significant. The Purchase Agreement includes a Use and Occupancy Agreement (the “U&O”) between the Seller and the Purchaser. The U&O provides the Purchaser with access to several of the Seller's facilities for a minimum period of 12 months at agreed upon payments. The Company will account for its equity interest in the Purchaser as an equity method investment as of the Closing Date. The Company has no plans to dispose of its equity interest. 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 9 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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. 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. 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): Employee Termination Costs and Other Liability balance at December 31, 2025 $ 2,601 Cash payments ( 2,601 ) Liability balance at March 31, 2026 $ — Restructuring charges were $ 4.5 million during the three months ended March 31, 2025, consisting 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): As of March 31, 2026 Total Level 1 Level 2 Level 3 Assets: Cash and cash equivalents: Money market funds $ 116,715 $ 116,715 $ — $ — U.S. Treasury securities 7,977 7,977 — — Marketable securities: Commercial paper 1,420 — 1,420 — U.S. Treasury securities 129,200 129,200 — — Corporate bonds 81,169 — 81,169 — Marketable equity securities 17,803 17,803 — — Investments: Synlogic, Inc. warrants (1) 104 — 104 — Marketable equity securities 1,286 1,286 — — Total assets $ 355,674 $ 272,981 $ 82,693 $ — Liabilities: Accrued expenses and other current liabilities: Contingent consideration $ 5,438 $ — $ — $ 5,438 Other non-current liabilities: Contingent consideration 252 — — 252 Total liabilities $ 5,690 $ — $ — $ 5,690 10 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) December 31, 2025 Total Level 1 Level 2 Level 3 Assets: Cash and cash equivalents: Money market funds $ 146,136 $ 146,136 $ — $ — Marketable securities: Commercial paper 4,060 — 4,060 — U.S. Treasury securities 118,038 118,038 — — Corporate bonds 114,666 — 114,666 — Marketable equity securities 18,654 18,654 — — Investments: Synlogic, Inc. warrants (1) 190 — 190 — Marketable equity securities 1,562 1,562 — — Other non-current assets: Notes receivable 7,126 — — 7,126 Total assets $ 410,432 $ 284,390 $ 118,916 $ 7,126 Liabilities: Accrued expenses and other current liabilities: Contingent consideration $ 5,438 $ — $ — $ 5,438 Other non-current liabilities: Contingent consideration 252 — — 252 Total liabilities $ 5,690 $ — $ — $ 5,690 (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 three months ended March 31, 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 three months ended March 31, 2026 or 2025. 11 Table of Contents 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 three months ended March 31 (in thousands): Notes Receivable Contingent Consideration Balance at January 1, 2026 $ 7,126 $ 5,690 Additions — — Change in fair value ( 7,126 ) — Settlements and payments — — Balance at March 31, 2026 $ — $ 5,690 Balance at January 1, 2025 $ 1,843 $ 9,922 Additions 75 — Change in fair value 50 ( 1,302 ) Settlements and payments ( 50 ) — Transfers into Level 3 6,983 — Balance at March 31, 2025 $ 8,901 $ 8,620 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 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 three months ended March 31, 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 three months ended March 31, 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 March 31, 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. 12 Table of Contents 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 three months ended March 31, 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: March 31, 2026 December 31, 2025 Contingent Consideration Liability Valuation Technique Unobservable Input Range Range Earnout payments (FGen and Dutch DNA acquisitions) Probability-weighted present value Probability of payment 5 % - 10 % 5 % - 10 % Discount rate 15.7 % 14.9 % 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 months ended March 31, 2026, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies. During the three months ended March 31, 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. No impairment losses related to Simple Agreements for Future Equity (“SAFEs”) were recorded during the three months ended March 31, 2026 or 2025, respectively. 13 Table of Contents 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): As of March 31, 2026 Amortized Cost Unrealized Gains Unrealized Losses Fair Value U.S. Treasury securities $ 137,088 $ 91 $ ( 1 ) $ 137,178 Corporate bonds 81,211 19 ( 62 ) 81,168 Commercial paper 1,419 1 — 1,420 Marketable equity securities — — — 17,803 Total cash equivalents and marketable securities 219,718 111 ( 63 ) 237,569 Less: cash equivalents ( 7,977 ) — — ( 7,977 ) Marketable securities $ 211,741 $ 111 $ ( 63 ) $ 229,592 December 31, 2025 Amortized Cost Unrealized Gains Unrealized Losses Fair Value U.S. Treasury securities $ 117,919 $ 171 ( 52 ) 118,038 Corporate bonds 114,640 147 ( 121 ) 114,666 Commercial paper 4,079 — ( 19 ) 4,060 Marketable equity securities — — — 18,654 Total marketable securities 236,638 318 ( 192 ) 255,418 Less: cash equivalents — — — — Marketable securities $ 236,638 $ 318 $ ( 192 ) $ 255,418 The amortized cost and estimated fair value of marketable debt securities at March 31, 2026, including $ 8.0 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands): Amortized cost Fair value Due within one year $ 179,182 $ 179,222 Due after one year through five years 40,536 40,544 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. The Company accounts for its investments in Platform Ventures under the equity method. Such investments had a carrying value of zero as of March 31, 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 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 14 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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): As of March 31, 2026 As of December 31, 2025 SAFEs $ 2,188 $ 2,188 Non-marketable equity securities 11,125 11,125 Marketable equity securities 1,286 1,562 Synlogic warrants 104 191 Total $ 14,703 $ 15,066 The components of loss on investments for each period were as follows (in thousands): Three Months Ended March 31, 2026 2025 Impairment charges $ — $ ( 1,844 ) Unrealized losses recognized on marketable equity securities and warrants ( 1,214 ) ( 1,849 ) Total loss on investments $ ( 1,214 ) $ ( 3,693 ) The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of March 31, 2026, including cumulative unrealized losses, were as follows (in thousands): As of March 31, 2026 Total initial cost $ 109,460 Impairment charges ( 91,806 ) Downward adjustments from observable price changes ( 4,341 ) Carrying value $ 13,313 7. Variable Interest Entities With respect to the Company’s investments in Motif, Allonnia, Genomatica, Arcaea, BiomEdit, Verb Biotics, and Ayana Bio, the Company has concluded these entities represent variable interest entities (such entities, the “VIEs”). 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 15 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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 March 31, 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): As of March 31, 2026 2025 Cash and cash equivalents $ 143,864 $ 312,420 Restricted cash included in prepaid expenses and other current assets (1) 6,883 7,943 Restricted cash included in other non-current assets (1) 37,922 35,042 Total cash, cash equivalents and restricted cash $ 188,669 $ 355,405 (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. 16 Table of Contents 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): Three Months Ended March 31, 2026 2025 Supplemental disclosure of non-cash investing and financing activities: Purchases of property and equipment included in accounts payable and accrued expenses $ 179 $ 96 Property, Plant and Equipment, net Property, plant and equipment, net consisted of the following (in thousands): As of March 31, As of December 31, 2026 2025 Lab equipment $ 140,681 $ 143,182 Leasehold improvements 138,289 140,513 Buildings and facilities 49,760 49,760 Construction in progress 4,453 192 Computer equipment and software 7,305 9,056 Furniture and fixtures 5,848 6,520 Land 6,060 6,060 Total property, plant and equipment 352,396 355,283 Less: Accumulated depreciation ( 189,376 ) ( 187,912 ) Property, plant and equipment, net $ 163,020 $ 167,371 Capitalization The following table presents the Company’s authorized, issued, and outstanding common stock as of the dates indicated: Authorized Issued Outstanding Common stock as of March 31, 2026: Class A 10,500,000,000 53,159,223 50,254,065 Class B 4,500,000,000 8,974,855 8,406,723 Class C 800,000,000 3,000,000 3,000,000 15,800,000,000 65,134,078 61,660,788 Common stock as of December 31, 2025: Class A 10,500,000,000 49,694,610 46,791,082 Class B 4,500,000,000 8,985,839 8,416,216 Class C 800,000,000 3,000,000 3,000,000 15,800,000,000 61,680,449 58,207,298 17 Table of Contents 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 March 31, 2026, the Company has issued 1.9 million shares of Class A common stock under the Sales Agreement for net proceeds of $ 18.1 million. 9. Intangible Assets, net Intangible assets, net consisted of the following (in thousands): Gross Carrying Value (1) Accumulated Amortization (1) Net Carrying Value Weighted Average Amortization Period (in Years) March 31, 2026: Developed technology $ 99,928 $ ( 51,068 ) $ 48,860 7.3 December 31, 2025: Developed technology $ 100,610 $ ( 47,128 ) $ 53,482 7.3 (1) Gross carrying value and accumulated amortization include the impact of foreign currency translation adjustments. Amortization expense was $ 4.2 million and $ 4.2 million for the three months ended March 31, 2026 and 2025, respectively. As of March 31, 2026, estimated future amortization expense for identifiable intangible assets is as follows (in thousands): Remainder of 2026 $ 12,402 2027 10,244 2028 2,941 2029 2,941 2030 2,941 Thereafter 17,391 Total $ 48,860 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. 18 Table of Contents 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): Three Months Ended March 31, 2026 2025 Research and development $ 8,023 $ 8,993 General and administrative 7,403 7,424 Cost of other revenue 427 969 Total $ 15,853 $ 17,386 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 March 31, 2026, there were 3,625,465 shares and 292,639 shares available for future issuance under the 2021 Plan and the 2022 Inducement Plan, respectively. Time-based Stock Options A summary of stock option activity for options that are subject to time-based vesting conditions for the three months ended March 31, 2026 is presented below: Number of Shares Weighted Average Exercise Price per Share Weighted Average Remaining Contractual Term (in Years) Aggregate Intrinsic Value (1) (in Thousands) Outstanding as of December 31, 2025 366,567 $ 15.38 Granted — — Forfeited — — Outstanding as of March 31, 2026 366,567 15.38 8.70 $ — Exercisable as of March 31, 2026 136,014 24.74 8.16 — (1) The aggregate intrinsic value is calculated as the difference between the Company's closing stock price on the last trading day of the quarter and the exercise prices, multiplied by the number of in-the-money stock options. There were no stock option exercises during the three months ended March 31, 2026 and 2025, respectively. As of March 31, 2026, there was $ 1.3 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 2.0 years. 19 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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 three months ended March 31, 2026 is presented below: Number of Shares Weighted Average Grant Date Fair Value Nonvested as of December 31, 2025 1,262,853 $ 55.07 Granted 591,007 7.05 Vested ( 346,073 ) 36.08 Forfeited ( 129,381 ) 48.45 Nonvested as of March 31, 2026 1,378,406 39.87 The weighted average grant date fair value of RSUs granted during the three months ended March 31, 2026 and 2025 was $ 7.05 and $ 7.95 , respectively. As of March 31, 2026, there was $ 46.6 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 1.6 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. A summary of PSU activity for the three months ended March 31, 2026 is presented below: Number of Shares Weighted Average Grant Date Fair Value Nonvested as of December 31, 2025 4,407,287 $ 8.06 Granted 3,078,611 6.38 Vested ( 3,107,417 ) 8.04 Forfeited ( 1,362,346 ) 8.05 Nonvested as of March 31, 2026 3,016,135 7.05 As of March 31, 2026, there was $ 20.0 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately 1.0 year, assuming a 100% PSU achievement rate. Actual expense recognized may vary based on the final achievement rate. 20 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) Earnouts Earnout shares represent equity awards, primarily in the form of restricted stock, granted to existing employees of the Company as of the closing date of the Company’s merger with Soaring Eagle Acquisition Corp. (“SRNG”) on September 16, 2021 (the “SRNG Closing Date”). These earnout shares are subject to the same time-based vesting and performance conditions (change in control or an initial public offering) as the underlying awards, including provisions related to vesting and termination. Additionally, the earnout shares are subject to a market condition, which is satisfied when the trading price of the Company's common stock is greater than or equal to $ 500 , $ 600 , $ 700 and $ 800 per share for any 20 trading days within a 30 consecutive trading day period, on or before the fifth anniversary of the SRNG Closing Date (collectively, the “Earnout Targets”). The first Earnout Target of $ 500 per share was met on November 15, 2021. No earnout shares vested or were forfeited during the three months ended March 31, 2026. As of March 31, 2026, there were 551,277 nonvested earnout shares with a weighted average grant date fair value of $ 510.78 . As of March 31, 2026, there was zero unrecognized compensation expense related to earnout shares. 12. Revenue Recognition Disaggregation of Revenue The following table sets forth the percentage of revenues by industry based on total revenue: Three Months Ended March 31, 2026 2025 Pharmaceutical and biotechnology 38 % 31 % Government and defense 35 16 Agriculture 13 41 Food and nutrition 7 4 Industrial and environment 7 7 Consumer and technology — 1 Total revenue 100 % 100 % 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 three months ended March 31, 2026 and 2025, but continues to recognize non-cash revenue from prior contracts. Revenue recognized relating to non-cash consideration was $ 0.5 million and $ 8.7 million for the three months ended March 31, 2026 and 2025, respectively. The Company’s total revenue is primarily generated from customers located in the United States. For the three months ended March 31, 2026 and 2025, U.S. customers accounted for 66 % and 81 %, respectively. For the three months ended March 31, 2026 and 2025, customers from Denmark accounted for 13 % 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 March 31, 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 balance of unbilled accounts receivable, included in accounts receivable, net in the accompanying condensed consolidated balance sheets, was $ 11.4 million and $ 14.5 million as of March 31, 2026 and December 31, 2025, respectively. 21 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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 three months ended March 31, 2026, the Company recognized $ 9.2 million of revenue that was included in the contract liabilities balance of $ 94.1 million as of December 31, 2025. During the three months ended March 31, 2025, the Company recognized $ 22.8 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 March 31, 2026 and December 31, 2025 was $ 127.4 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 March 31, 2026, approximately $ 15.8 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; $ 40.8 million between 2026 and 2027; $ 63.2 million between 2026 and 2028; $ 3.4 million between 2026 and 2029; and $ 4.2 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 the 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. 22 Table of Contents 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): Three Months Ended March 31, 2026 2025 Revenue $ 19,474 $ 38,230 Costs and operating expenses: Cost of other revenue (1) 2,672 3,121 Research and development (1) 30,105 48,670 General and administrative (1) 12,723 19,654 Stock-based compensation (2) 16,708 17,713 Depreciation and amortization 12,799 14,822 Restructuring charges (3) — 4,466 Carrying cost of excess space (net of sublease income) (4) 15,842 11,674 Merger and acquisition related expense (income) (5) — ( 918 ) Other (income) expense, net (6) 4,764 2,250 Loss from continuing operations before income taxes $ ( 76,139 ) $ ( 83,222 ) (1) The costs and operating expenses exclude expenses which are separately captioned below. (2) Includes $ 0.9 million and $ 0.4 million in employer payroll taxes for three months ended March 31, 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 and acquisitions, 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: As of March 31, 2026 2025 Unvested PSUs 3,016,135 4,115,270 Unvested RSUs 1,378,406 3,710,189 Earnout shares (1) 3,793,063 3,794,111 Warrants to purchase Class A common stock 1,295,622 1,295,622 Outstanding stock options 366,567 761,312 Escrow shares (2) — 6,647 9,849,793 13,683,151 (1) Represents employee and non-employee earnout shares for which the service-based and/or market-based vesting conditions have not been satisfied. (2) Represents restricted common stock issued in connection with asset acquisitions, held in escrow for indemnification purposes, and subject to forfeiture. 23 Table of Contents 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): As of March 31, 2026 As of December 31, 2025 Deferred revenue, current and non-current: Allonnia $ 36,495 $ 36,495 Arcaea 28,413 28,413 $ 64,908 $ 64,908 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): Three Months Ended March 31, 2025 Revenue: Genomatica $ 274 Ayana Bio 240 Allonnia 1 BiomEdit 7,583 $ 8,098 During the three months ended March 31, 2026, the Company recognized zero revenue from related parties. In February 2025, the Company and Motif mutually agreed to terminate Motif’s sublease of certain Company facility space whereby Motif paid the Company a termination fee of $ 1.6 million. The termination fee was recorded as sublease income, net of certain costs. Sublease income is recognized as a reduction of operating lease costs reported in general and administrative expenses. In March 2025, the Company and BiomEdit mutually terminated certain agreements entered into in April 2022, which had granted BiomEdit a license to certain of the Company’s intellectual property and established the terms under which the Company would provide technical research and development services to BiomEdit. In exchange for the Company’s contribution of intellectual property and access to its platform, the Company received shares of common stock in BiomEdit valued at $ 10.0 million. The non-refundable fair value of this equity, considered non-cash consideration under ASC 606, was accounted for as material rights in accordance with ASC 606. These material rights related to BiomEdit’s license to certain applicable patents and other intellectual property that the parties intended to develop under technical development plans. This amount was recorded as deferred revenue for the future license rights and is recognized as revenue either as the Company performs qualifying services for BiomEdit or, if applicable, when such rights expire upon termination of the agreements. As a result of the termination of certain agreements with BiomEdit, the Company no longer has any obligation to perform services for BiomEdit, and the remaining $ 7.5 million in material rights deferred revenue was recognized in full as revenue during the three months ended March 31, 2025. BiomEdit is no longer considered a significant related party due to a reduction of the Company’s equity ownership interest that occurred during the three months ended June 30, 2025. Refer to Note 6 for additional details on the Company’s investments and equity method investments held in its related parties. 24 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 16. Subsequent Events Refer to Note 2 for a description of the Biosecurity Divestiture, which closed subsequent to March 31, 2026. Additionally, 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. 25 Table of Contents