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, As of December 31, 2025 2024 Assets Current assets: Cash and cash equivalents $ 312,420 $ 561,572 Marketable securities 204,502 — Accounts receivable, net 26,293 21,857 Accounts receivable - related parties 877 586 Prepaid expenses and other current assets 20,442 18,729 Total current assets 564,534 602,744 Property, plant and equipment, net 197,828 203,720 Operating lease right-of-use assets 383,394 394,435 Investments 32,173 48,704 Intangible assets, net 68,756 72,510 Other non-current assets 46,778 55,336 Total assets $ 1,293,463 $ 1,377,449 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 11,267 $ 14,169 Deferred revenue (includes $ 391 and $ 795 from related parties) 33,653 27,710 Accrued expenses and other current liabilities 70,747 65,387 Total current liabilities 115,667 107,266 Non-current liabilities: Deferred revenue, net of current portion (includes $ 64,786 and $ 72,260 from related parties) 80,378 98,783 Operating lease liabilities, non-current 434,561 438,766 Other non-current liabilities 15,430 16,576 Total liabilities 646,036 661,391 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) 5 5 Additional paid-in capital 6,576,786 6,555,416 Accumulated deficit ( 5,928,514 ) ( 5,837,557 ) Accumulated other comprehensive loss ( 850 ) ( 1,806 ) Total stockholders’ equity 647,427 716,058 Total liabilities and stockholders’ equity $ 1,293,463 $ 1,377,449 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, 2025 2024 Cell Engineering revenue (1) $ 38,230 $ 27,889 Biosecurity revenue 10,088 10,055 Total revenue 48,318 37,944 Costs and operating expenses: Cost of Biosecurity revenue 7,957 9,202 Cost of other revenue 4,090 — Research and development 70,923 136,457 General and administrative 49,043 70,287 Restructuring charges 5,273 — Total operating expenses 137,286 215,946 Loss from operations ( 88,968 ) ( 178,002 ) Other income (expense): Interest income, net 6,081 11,711 Loss on investments ( 3,693 ) ( 2,544 ) Change in fair value of warrant liabilities — 940 Other income (expense), net ( 4,289 ) 2,015 Total other income (expense) ( 1,901 ) 12,122 Loss before income taxes ( 90,869 ) ( 165,880 ) Income tax expense 88 31 Net loss $ ( 90,957 ) $ ( 165,911 ) Net loss per share: Basic $ ( 1.68 ) $ ( 3.31 ) Diluted $ ( 1.68 ) $ ( 3.32 ) Weighted average common shares outstanding: Basic 54,241,619 50,111,460 Diluted 54,241,619 50,133,366 Comprehensive loss: Net loss $ ( 90,957 ) $ ( 165,911 ) Other comprehensive (loss) income: Foreign currency translation adjustment 849 ( 3,035 ) Unrealized gains on available-for-sale securities 107 — Total other comprehensive (loss) income 956 ( 3,035 ) Comprehensive loss $ ( 90,001 ) $ ( 168,946 ) (1) Includes related party revenue of $ 8,098 and $ 733 for the three months ended March 31, 2025 and 2024, 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, 2024 Common Stock Shares Amount Additional Paid-In Capital Accumulated Deficit Accumulated Other Comprehensive (Loss) Income Total Stockholders’ Equity Balance as of December 31, 2023 50,032,873 $ 5 $ 6,386,191 $ ( 5,290,528 ) $ 1,484 $ 1,097,152 Issuance of common stock upon exercise or vesting of equity awards 454,756 — 529 — — 529 Settlement of contingent consideration 24,657 — 1,877 — — 1,877 Issuance of common stock for asset acquisitions 328,321 — 15,876 — — 15,876 Stock-based compensation expense — — 40,782 — — 40,782 Other comprehensive loss — — — — ( 3,035 ) ( 3,035 ) Net loss — — — ( 165,911 ) — ( 165,911 ) Balance as of March 31, 2024 50,840,607 $ 5 $ 6,445,255 $ ( 5,456,439 ) $ ( 1,551 ) $ 987,270 Three Months Ended March 31, 2025 Common Stock Shares Amount Additional Paid-In Capital Accumulated Deficit Accumulated Other Comprehensive (Loss) Income 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. 3 Table of Contents Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Statements of Cash Flows (unaudited) (in thousands) Three Months Ended March 31, 2025 2024 Cash flows from operating activities: Net loss $ ( 90,957 ) $ ( 165,911 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 15,366 12,869 Stock-based compensation 20,431 40,782 Loss on investments 3,693 2,544 Change in fair value of notes receivable 5,285 — Change in fair value of warrant liabilities — ( 940 ) Change in fair value of contingent consideration ( 1,302 ) ( 926 ) Non-cash lease expense 7,379 5,637 Non-cash in-process research and development — 16,816 Other non-cash activity 149 ( 442 ) Changes in operating assets and liabilities: Accounts receivable ($(291) and $372 from related parties) ( 4,693 ) ( 6,770 ) Prepaid expenses and other current assets 462 1,154 Operating lease right-of-use assets 3,675 — Other non-current assets ( 167 ) ( 707 ) Accounts payable, accrued expenses and other current liabilities 6,419 10,871 Deferred revenue, current and non-current ($(7,878) and $(223) from related parties) ( 12,471 ) ( 2,912 ) Operating lease liabilities, current and non-current ( 4,790 ) ( 4,097 ) Other non-current liabilities — 2,773 Net cash used in operating activities ( 51,521 ) ( 89,259 ) Cash flows from investing activities: Purchases of marketable debt securities ( 191,182 ) — Purchases of property and equipment ( 7,622 ) ( 6,710 ) Business acquisition — ( 5,400 ) Other 120 — Net cash used in investing activities ( 198,684 ) ( 12,110 ) Cash flows from financing activities: Proceeds from exercise of stock options — 70 Principal payments on finance leases ( 207 ) ( 294 ) Contingent consideration payment — ( 621 ) Net cash used in financing activities ( 207 ) ( 845 ) Effect of foreign exchange rates on cash and cash equivalents 74 ( 157 ) Net decrease in cash, cash equivalents and restricted cash ( 250,338 ) ( 102,371 ) Cash and cash equivalents, beginning of period 561,572 944,073 Restricted cash, beginning of period 44,171 45,511 Cash, cash equivalents and restricted cash, beginning of period 605,743 989,584 Cash and cash equivalents, end of period 312,420 840,440 Restricted cash, end of period 42,985 46,773 Cash, cash equivalents and restricted cash, end of period $ 355,405 $ 887,213 The accompanying notes are an integral part of these condensed consolidated financial statements. 4 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 The mission of Ginkgo Bioworks Holdings, Inc. (“Ginkgo” or the “Company”) is to make biology easier to engineer. The Company provides biological research and development services for customers across multiple markets and industries. Since inception, the Company has devoted its efforts to improving its platform for programming cells to enable customers to leverage biology to create impactful products across a range of industries. The Company’s platform comprises (i) equipment, robotic automation, software, data pipelines and tools, and standard operating procedures for high throughput cell engineering, fermentation, and analytics (referred to collectively as the “Foundry”), (ii) a library of proprietary biological assets and associated performance data (referred to collectively as “Codebase”), and (iii) the Company’s team of expert users, developers and operators of the Foundry and Codebase. The Company’s biosecurity business (“Biosecurity”) consists of the Company’s biomonitoring and bioinformatics support services, offered to both government and non-government customers through the Company's two core offerings: Canopy and Horizon, which provide services to government and commercial customers working to identify, monitor, prevent, mitigate, and ultimately protect humanity from biological threats. Basis of Presentation The accompanying condensed consolidated financial statements have been prepared in conformity with the rules and regulations of the Securities and Exchange Commission 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 2024 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. 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, 2025 as compared to the significant accounting policies described in Note 2 to the Company’s 2024 consolidated financial statements included in the 2024 Annual Report. Marketable Securities Beginning in the three months ended March 31, 2025, the Company began investing its excess cash in marketable debt securities. All debt securities are classified as available-for-sale at the time of purchase. Available-for-sale debt securities, including those with maturities extending beyond one year, are classified as current assets on the balance sheet due to their highly liquid nature and because they are considered available for use in current operations. Debt securities that are highly liquid and have original maturities of three months or less at the time of acquisition are classified as cash equivalents on the 5 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) condensed consolidated balance sheet. The Company considers securities to be highly liquid if they can be readily converted to cash with an insignificant risk of changes in value, typically due to active markets and high credit quality. Unrealized gains and losses on available-for-sale marketable debt securities that are not related to credit losses are included in other comprehensive (loss) income in the condensed consolidated statements of operations and comprehensive loss. Amortization of premium or accretion of discount, along with interest income earned on debt securities, is included in interest income, net. Realized gains and losses, if any, are included in other income (expense), net, and the cost of securities sold is determined using the specific-identification method. As of the balance sheet date, the Company evaluates its debt securities in an unrealized loss position to determine the extent of the loss, if any, that is attributable to expected credit losses. Expected credit losses on debt securities are recorded as an allowance on the balance sheet, with an offsetting amount recognized in other income (expense), net, in the condensed consolidated statements of operations and comprehensive loss. To date, the Company has not recorded any credit losses on its marketable debt securities. Marketable securities also includes equity securities of publicly-traded companies that are considered to be available for use in current operations. Equity securities of publicly-traded companies that are not considered to be available for use in current operations are presented within investments on the condensed consolidated balance sheet. 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 2024 consolidated financial statements included in the 2024 Annual Report. 2. Acquisitions On October 3, 2023, and in connection with the bankruptcy filing of the Company’s former subsidiary, Zymergen (the “Zymergen Bankruptcy”), the Company entered into an asset purchase agreement with Zymergen (the “Zymergen APA”) as the stalking horse bidder under Section 363 of the U.S. Bankruptcy Code to acquire exclusive rights to substantially all of Zymergen’s intellectual property assets and certain other assets. On January 18, 2024, the Company, through certain of its affiliates, completed its acquisition of substantially all of Zymergen’s assets under the Zymergen APA, and on February 5, 2024, Zymergen’s plan of liquidation was confirmed by the Bankruptcy Court. All of the Company’s interests in the Zymergen entities were extinguished and terminated as of February 23, 2024. The acquisition under the Zymergen APA was accounted for as a business combination in accordance with ASC 805 and was not material to the Company’s consolidated financial statements. The total cash purchase price was $ 6.2 million, with $ 5.4 million paid at closing and $ 0.8 million released from escrow. The allocation of the purchase price to the assets acquired and liabilities assumed as of the acquisition date primarily includes $ 19.9 million of operating lease right-of-use assets, $ 6.0 million of property and equipment, and $ 19.9 million of operating lease liabilities. No goodwill or intangible assets were recognized. Transaction costs associated with the Zymergen APA were not material for the three months ended March 31, 2024. In the three months ended March 31, 2024, the Company issued 328,321 shares of Class A common stock to acquire certain assets, which did not meet the definition of a business for accounting purposes. The assets acquired consisted of intellectual property with an aggregate estimated fair value of $ 16.9 million, all of which was expensed as in-process research and development in the accompanying condensed consolidated statements of operations and comprehensive loss during the period, as the assets did not have an alternative use. 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 Board of Directors, approved and commenced a restructuring plan. This plan includes 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 continued through March 31, 2025, with further reductions expected for the remainder of 2025. All workforce reductions are expected to be substantially completed 6 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) in 2025, subject to compliance with applicable laws. The Company plans to consolidate certain facilities through various actions, including combining office and laboratory operations into fewer locations, subleasing unused or underutilized facilities, and has taken or plans to take other related measures, such as the sale of its subsidiary, Altar SAS, in the third quarter of 2024. While the Company has substantially completed the majority of its facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities may extend beyond 2025 or may not occur prior to termination of such lease, depending on market conditions. Additionally, restructuring expenses related to potential asset impairments or contract amendments or terminations for any facilities no longer in use or underutilized could be material. The costs for the reduction in force are expected to range from $ 24.0 million to $ 26.0 million primarily in the Cell Engineering segment and consist of cash severance and related costs. The employee termination costs are recognized as of the communication date to employees, given (i) the Company instituted a one-time employee termination benefit related to its restructuring, and (ii) the employees will not be retained to render service beyond a minimum retention period. 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. During the three months ended March 31, 2025, the Company incurred $ 5.3 million of employee termination benefits and other costs, which are recorded as “Restructuring charges” in the condensed consolidated statements of operations and comprehensive loss. 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 sheet (in thousands): Employee Termination Costs and Other Liability balance at December 31, 2024 $ 2,854 Expenses incurred 5,273 Cash payments ( 3,772 ) Liability balance at March 31, 2025 $ 4,355 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): 7 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) As of March 31, 2025 Total Level 1 Level 2 Level 3 Assets: Cash and cash equivalents: Money market funds $ 135,564 $ 135,564 $ — $ — Commercial paper 39,526 — 39,526 — U.S. Treasury securities 115,640 115,640 — — Corporate bonds 1,417 — 1,417 — Marketable securities: Commercial paper 23,462 — 23,462 — U.S. Treasury securities 99,064 99,064 — — Corporate bonds 69,138 — 69,138 — Marketable equity securities (1) 12,838 12,838 — — Investments: Synlogic, Inc. warrants (2) 211 — 211 — Marketable equity securities 2,899 2,899 — — Other non-current assets: Notes receivable 8,901 — — 8,901 Total assets $ 508,660 $ 366,005 $ 133,754 $ 8,901 Liabilities: Accrued expenses and other current liabilities: Contingent consideration $ 5,438 $ — $ — $ 5,438 Other non-current liabilities: Contingent consideration 3,182 — — 3,182 Total liabilities $ 8,620 $ — $ — $ 8,620 As of December 31, 2024 Total Level 1 Level 2 Level 3 Assets: Cash and cash equivalents: Money market funds $ 521,457 $ 521,457 $ — $ — Investments: Synlogic, Inc. warrants (2) 238 — 238 — Marketable equity securities 17,559 17,559 — — Other non-current assets: Notes receivable 14,170 — 12,327 1,843 Total assets $ 553,424 $ 539,016 $ 12,565 $ 1,843 Liabilities: Accrued expenses and other current liabilities: Contingent consideration $ 5,438 $ — $ — $ 5,438 Other non-current liabilities: Contingent consideration 4,484 — — 4,484 Total liabilities $ 9,922 $ — $ — $ 9,922 8 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) (1) These securities were previously reported within investments on the condensed consolidated balance sheet and, as of March 31, 2025, are classified as current assets, as they are considered to be available for use in current operations. (2) 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. During the three months ended March 31, 2024, transfers from Level 2 to Level 1 occurred due to the lapse of regulatory sales restrictions on marketable equity securities. There were no other transfers between Levels 1, 2, or 3 during the three months ended March 31, 2025 or 2024. 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 Private Placement Warrants Contingent Consideration 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 Balance at January 1, 2024 $ 14,129 $ 1,846 $ 24,273 Additions 50 — — Change in fair value 961 ( 309 ) ( 926 ) Settlements and payments — — ( 2,753 ) Balance at March 31, 2024 $ 15,140 $ 1,537 $ 20,594 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., 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. As of March 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 and a risk-adjusted discount rate. These inputs reflect the Company’s own assumptions and, therefore, represent a Level 3 measurement within the fair value hierarchy. As of December 31, 2024, the Company used the yield method to value the senior secured note. Under this method, the estimated future cash flows, consisting of principal and interest payments, are discounted to present value using an applicable market yield or discount rate. The market yield is determined using a corporate bond yield curve corresponding to the issuer’s credit rating category and is considered an observable market input, representing a Level 2 measurement within the fair value hierarchy. Increases or decreases in the market yield or discount rate would result in a decrease or increase, respectively, in the fair value measurement. 9 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) The Company also holds 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 March 31, 2025 and December 31, 2024 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, 2025, the Company’s notes receivable had an unpaid principal balance of $ 24.9 million and a fair value of $ 8.9 million, compared to an unpaid principal balance of $ 25.1 million and a fair value of $ 14.2 million as of December 31, 2024. 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. The Company can settle a majority of its contingent consideration liabilities in cash or shares of Class A common stock at the Company’s election with the remainder payable in cash. During the three months ended March 31, 2024, the Company settled $ 2.8 million in contingent consideration liabilities through payment of $ 0.9 million in cash and vesting of 31,127 shares of restricted stock valued at $ 1.9 million. No contingent consideration was settled during the three months ended March 31, 2025. 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, 2025 December 31, 2024 Contingent Consideration Liability Valuation Technique Unobservable Input Range Range Earnout payments (FGen and Dutch DNA acquisitions) Probability-weighted present value Probability of payment 5 % - 25 % 5 % - 50 % Discount rate 11.7 % 9.3 % Earnout payments (Dutch DNA acquisition) Discounted cash flow Projected years of payments 2028 - 2031 2028 - 2031 Discount rate 10.6 % 10.6 % 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. 10 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) During the three months ended March 31, 2025, the Company recorded an impairment loss 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 March 31, 2024, the Company recorded impairment losses of $ 5.2 million related to Simple Agreements for Future Equity (“SAFEs”). Fair value was generally estimated using the scenario-based method, in which various payout scenarios were probability-weighted and discounted to present value. No impairment losses related to SAFEs were recorded during the three months ended March 31, 2025. 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, 2025 Amortized Cost Unrealized Gains Unrealized Losses Fair Value U.S. Treasury securities $ 214,662 $ 46 $ ( 4 ) $ 214,704 Corporate bonds 70,501 59 ( 5 ) 70,555 Commercial paper 62,977 17 ( 6 ) 62,988 Marketable equity securities 12,838 Total cash equivalents and marketable securities 348,140 122 (15) 361,085 Less: cash equivalents (156,591) — 8 (156,583) Marketable securities $ 191,549 $ 122 $ (7) $ 204,502 The amortized cost and estimated fair value of marketable debt securities, including $156.6 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands): As of March 31, 2025 Amortized cost Fair value Due within one year $ 315,836 $ 315,900 Due after one year through five years 32,304 32,347 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, Inc. (“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. 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 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 11 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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, 2025 As of December 31, 2024 SAFEs $ 16,689 $ 16,689 Non-marketable equity securities 12,374 14,218 Marketable equity securities 2,899 17,559 Synlogic warrants 211 238 Total $ 32,173 $ 48,704 The components of loss on investments for each period were as follows (in thousands): Three Months Ended March 31, 2025 2024 Impairment charges $ ( 1,844 ) $ ( 5,212 ) Unrealized gains (losses) recognized on marketable equity securities and warrants ( 1,849 ) 2,668 Total loss on investments $ ( 3,693 ) $ ( 2,544 ) The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of March 31, 2025, including cumulative unrealized losses, were as follows (in thousands): As of March 31, 2025 Total initial cost $ 107,996 Impairment charges ( 77,305 ) Downward adjustments from observable price changes ( 1,628 ) Carrying value $ 29,063 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 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 12 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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, 2025 and December 31, 2024, 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, 2025 2024 Cash and cash equivalents $ 312,420 $ 840,440 Restricted cash included in prepaid expenses and other current assets (1) 7,943 3,328 Restricted cash included in other non-current assets (1) 35,042 43,445 Total cash, cash equivalents and restricted cash $ 355,405 $ 887,213 (1) Includes 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. 13 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, 2025 2024 Supplemental disclosure of non-cash investing and financing activities: Purchases of property and equipment included in accounts payable and accrued expenses $ 96 $ 7,886 Common stock issued as settlement of contingent consideration liability — 1,877 Property, Plant and Equipment, net Property, plant and equipment, net consisted of the following (in thousands): As of March 31, As of December 31, 2025 2024 Lab equipment $ 148,815 $ 150,887 Leasehold improvements 140,407 135,964 Buildings and facilities 48,294 48,255 Construction in progress 1,453 1,984 Computer equipment and software 9,674 14,897 Furniture and fixtures 6,546 6,545 Land 6,060 6,060 Total property, plant and equipment 361,249 364,592 Less: Accumulated depreciation ( 163,421 ) ( 160,872 ) Property, plant and equipment, net $ 197,828 $ 203,720 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, 2025: Class A 10,500,000,000 45,955,211 43,075,350 Class B 4,500,000,000 9,193,344 8,622,896 Class C 800,000,000 3,000,000 3,000,000 15,800,000,000 58,148,555 54,698,246 Common stock as of December 31, 2024: Class A 10,500,000,000 45,575,423 42,696,585 Class B 4,500,000,000 9,239,682 8,669,200 Class C 800,000,000 3,000,000 3,000,000 15,800,000,000 57,815,105 54,365,785 14 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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, 2025: Developed technology $ 112,648 $ ( 43,892 ) $ 68,756 6.6 December 31, 2024: Developed technology $ 111,393 $ ( 38,883 ) $ 72,510 6.6 (1) Gross carrying value and accumulated amortization include the impact of cumulative foreign currency translation adjustments. Amortization expense was $ 4.7 million and $ 3.4 million for the three months ended March 31, 2025 and 2024, respectively. As of March 31, 2025, estimated future amortization expense for identifiable intangible assets is as follows (in thousands): Remainder of 2025 $ 14,235 2026 18,980 2027 11,344 2028 2,717 2029 2,717 Thereafter 18,763 Total $ 68,756 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. 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, 2025 2024 Research and development $ 8,993 $ 23,192 General and administrative 9,734 17,590 Cost of Biosecurity revenue 735 — Cost of other revenue 969 — Total $ 20,431 $ 40,782 15 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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, 2025, there were 2,319,438 shares and 224,083 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, 2025 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, 2024 267,520 $ 25.17 Forfeited ( 6,208 ) 92.08 Outstanding as of March 31, 2025 261,312 23.58 9.18 $ — Exercisable as of March 31, 2025 27,339 95.35 7.75 — (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. The aggregate intrinsic value of stock options exercised during the three months ended March 31, 2024 was $ 3.9 million. There were no stock option exercises during the three months ended March 31, 2025. As of March 31, 2025, there was $ 1.3 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 1.8 years. Market-based Stock Options In April 2024, the Company granted to each of the Company's four founders an option to purchase in aggregate 125,000 shares of Ginkgo's Class A common stock with an exercise price of $ 100 per share, subject both to time-based and market-based vesting criteria (the “Founder Options”). The market-based vesting is tied to the achievement of four specified stock price hurdles within a five-year period, with 10 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 200 , 10 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 300 , 20 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 400 and the remaining 60 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 500 . If the market-based criteria are achieved during the five-year period, the awards will vest on the five-year anniversary of the grant date. As of March 31, 2025, there was $ 3.2 million of unrecognized compensation expense related to the market-based options recognizable over a weighted-average period of 4.1 years. 16 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 2025 will vest in equal quarterly installments through January 2026. A summary of the RSU activity for the three months ended March 31, 2025 is presented below: Number of Shares Weighted Average Grant Date Fair Value Nonvested as of December 31, 2024 3,327,398 $ 69.00 Granted 1,119,363 7.95 Vested ( 332,364 ) 88.02 Forfeited ( 404,208 ) 64.01 Nonvested as of March 31, 2025 3,710,189 49.42 The weighted average grant date fair value of RSUs granted during the three months ended March 31, 2025 and 2024 was $ 7.95 and $ 48.40 , respectively. As of March 31, 2025, there was $ 154.9 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 2.3 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 are eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2025 cash flow targets. Recipients must remain employed through the date the applicable vested shares are distributed, which is expected to occur in March 2026. PSU achievement percentages may range from 0% to 100%. 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, 2025 is presented below: Number of Shares Weighted Average Grant Date Fair Value Granted 4,148,022 $ 7.81 Forfeited ( 32,752 ) 7.81 Nonvested as of March 31, 2025 4,115,270 7.81 As of March 31, 2025, there was $ 30.4 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately one year, assuming a 100% PSU achievement rate. Actual expense recognized may vary based on the final achievement rate. 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 SRNG on September 16, 2021 (the “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 17 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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 Closing Date (collectively, the “Earnout Targets”). The first Earnout Target of $ 500 per share was met on November 15, 2021. A summary of activity during the three months ended March 31, 2025 for the earnout shares is presented below: Number of Shares Weighted Average Grant Date Fair Value Nonvested as of December 31, 2024 552,457 $ 510.80 Vested ( 97 ) 533.60 Forfeited ( 35 ) 516.11 Nonvested as of March 31, 2025 552,325 510.80 As of March 31, 2025, there was $ 0.1 million of unrecognized compensation expense related to earnout shares recognizable over a weighted-average period of 0.3 years. 12. Revenue Recognition Disaggregation of Revenue The following table sets forth the percentage of Cell Engineering revenues by industry based on total Cell Engineering revenue: Three Months Ended March 31, 2025 2024 Agriculture 41 % 28 % Pharmaceutical and biotechnology 31 28 Government and defense 16 16 Industrial and environment 7 10 Food and nutrition 4 17 Consumer and technology 1 1 Total Cell Engineering revenue 100 % 100 % Cell Engineering 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, 2025 and 2024, but continues to recognize non-cash revenue from prior contracts. Cell Engineering revenue recognized relating to non-cash consideration was $ 8.7 million and $ 3.8 million for the three months ended March 31, 2025 and 2024, respectively. The Company’s total revenue is derived from customers located primarily in the United States. For the three months ended March 31, 2025 and 2024, the Company’s revenue from customers within the United States comprised 76 % and 70 %, respectively, of total revenue. 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, 2025 and December 31, 2024. 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 18 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) 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 $9.0 million and $11.3 million as of March 31, 2025 and December 31, 2024, 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 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. During the three months ended March 31, 2024, the Company recognized $ 13.8 million of revenue that was included in the contract liabilities balance of $ 202.5 million as of December 31, 2023. 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, 2025 and December 31, 2024 was $ 123.8 million and $ 85.8 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, 2025, approximately $ 37.5 million of the unsatisfied or partially satisfied performance obligations is expected to be recognized as revenue in 2025, based on the projected customer program end date; $ 10.3 million between 2025 and 2026; $ 50.0 million between 2025 and 2027; and $ 26.0 million between 2025 and 2028. 13. Segment Information The Company operates in two operating and reportable segments: Cell Engineering and Biosecurity. 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 segments are described as follows: • Cell Engineering consists of end-to-end cell engineering solutions and cell engineering tools offerings for biological R&D. The Company’s cell engineering platform includes two core assets: the Foundry, a highly efficient biology laboratory powered by proprietary workflows, custom software, robotic automation, and data science and analytics, and the Codebase, a collection of biological “parts” and a database of biological data used to program cells. The Cell Engineering segment includes costs incurred for the development, operation, expansion and enhancement of the Foundry and Codebase. Cell Engineering revenue is generated primarily through service fees and downstream value share in the form of milestone payments, royalties or equity interests. • Biosecurity consists of the Company’s biomonitoring and bioinformatics support services, offered to both government and non-government customers through the Company’s two core offerings: Canopy and Horizon. Biosecurity revenue is generated from fees for data, analytics, and services. The Company’s reportable segments are those 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 Chief Operating Officer, for the purpose of allocating resources and assessing financial performance. The CODM evaluates the financial performance of the Company’s segments based on segment operating income (loss). The CODM is primarily provided with the segment operating income (loss) 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 to each segment. For management reporting purposes, the 19 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) Company’s measure of segment operating income (loss) excludes the impact of stock-based compensation expense, depreciation and amortization, asset impairment charges, restructuring charges, costs associated with excess space, transaction and integration costs associated with planned, completed or terminated mergers and acquisitions, and acquired in-process research and development expenses. The Company has determined its significant segment expenses are cost of revenue for Biosecurity, research and development expenses for Cell Engineering, and general and administrative expenses for both segments, which are regularly provided to the CODM. The CODM is not provided with asset information by segment; 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 following table presents summary results of the Company’s reportable segments and a reconciliation of total segment operating loss to consolidated loss before income taxes (in thousands): Three Months Ended March 31, 2025 2024 Cell Engineering Revenue $ 38,230 $ 27,889 Costs and operating expenses: Cost of other revenue 3,121 — Research and development 48,670 81,898 General and administrative 18,027 38,244 Cell Engineering operating loss ( 31,588 ) ( 92,253 ) Biosecurity Revenue 10,088 10,055 Costs and operating expenses: Cost of Biosecurity revenue 7,223 9,202 Research and development — 120 General and administrative 8,050 11,951 Biosecurity operating loss ( 5,185 ) ( 11,218 ) Total segment operating loss ( 36,773 ) ( 103,471 ) Reconciling items to reconcile total segment operating loss to loss before income taxes: Stock-based compensation (1) 20,800 42,397 Depreciation and amortization 15,366 12,869 Restructuring charges (2) 5,273 — Carrying cost of excess space (net of sublease income) (3) 11,674 — Merger and acquisition related expense (income) (4) ( 918 ) 2,394 Acquired in-process research and development — 16,871 Other (income) expense, net (5) 1,901 ( 12,122 ) Loss before income taxes $ ( 90,869 ) $ ( 165,880 ) (1) Includes $ 0.4 million and $ 1.6 million in employer payroll taxes for the three months ended March 31, 2025 and 2024, respectively. (2) See Note 3 , Restructuring, for composition of costs. (3) 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. (4) 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) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs. 20 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) (5) 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 calculation of basic and diluted earnings per common share is as follows (in thousands, except share data): Three Months Ended March 31, 2025 2024 Numerator: Net loss, basic $ ( 90,957 ) $ ( 165,911 ) Change in fair value of contingent consideration common shares liability — 464 Net loss, diluted $ ( 90,957 ) $ ( 166,375 ) Denominator: Weighted average common shares outstanding, basic 54,241,619 50,111,460 Effect of dilutive securities: Contingent consideration common shares — 21,906 Weighted average common shares outstanding, diluted 54,241,619 50,133,366 Basic net loss per share $ ( 1.68 ) $ ( 3.31 ) Diluted net loss per share $ ( 1.68 ) $ ( 3.32 ) 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, 2025 2024 Unvested PSUs 4,115,270 — Unvested RSUs 3,710,189 5,967,596 Earnout shares (1) 3,794,111 3,803,377 Warrants to purchase Class A common stock 1,295,622 1,295,622 Outstanding stock options 761,312 104,125 Escrow shares (2) 6,647 18,266 13,683,151 11,188,986 (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. 21 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, 2025 As of December 31, 2024 Deferred revenue, current and non-current: Allonnia $ 36,472 $ 36,495 Arcaea 28,413 28,413 BiomEdit — 7,583 Genomatica 290 564 Ayana Bio 2 — $ 65,177 $ 73,055 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 2024 Cell Engineering revenue: Genomatica $ 274 $ 369 Ayana Bio 240 147 Allonnia 1 59 Motif — 19 BiomEdit 7,583 — Other equity investees — 139 $ 8,098 $ 733 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 of December 31, 2024, the Company had a remaining deferred revenue balance of $ 7.5 million related to the material rights with BiomEdit. 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. 22 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) Refer to Note 6 for additional details on the Company’s investments and equity method investments held in its related parties. 23 Table of Contents