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 June 30, 2026 As of December 31, 2025 Assets Current assets: Cash and cash equivalents $ 84,535 $ 167,202 Marketable securities 217,628 255,418 Accounts receivable, net 13,013 24,026 Accounts receivable - related parties — 229 Prepaid expenses and other current assets (includes $ 4,444 and zero from related parties) 17,359 24,963 Total current assets 332,535 471,838 Restricted cash and cash equivalents, non-current 84,565 38,138 Property, plant and equipment, net 157,185 167,371 Operating lease right-of-use assets 347,661 360,918 Investments 14,775 15,066 Equity method investments 7,615 — Intangible assets, net 44,387 53,482 Other non-current assets 1,323 9,029 Assets held for sale — 3,854 Total assets $ 990,046 $ 1,119,696 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 9,575 $ 10,566 Deferred revenue (includes $ 98 and $ 98 from related parties) 13,214 18,946 Accrued expenses and other current liabilities (includes $ 2,513 and zero from related parties) 49,951 66,458 Total current liabilities 72,740 95,970 Non-current liabilities: Deferred revenue, net of current portion (includes $ 64,810 and $ 64,787 from related parties) 76,537 75,182 Operating lease liabilities, non-current 404,113 417,078 Other non-current liabilities 16,372 22,876 Total liabilities 569,762 611,106 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 6,698,945 6,657,053 Accumulated deficit ( 6,279,617 ) ( 6,150,320 ) Accumulated other comprehensive income 950 1,851 Total stockholders’ equity 420,284 508,590 Total liabilities and stockholders’ equity $ 990,046 $ 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 June 30, Six Months Ended June 30, 2026 2025 2026 2025 Revenue (1) $ 20,156 $ 39,134 $ 39,630 $ 77,364 Costs and operating expenses: Cost of other revenue 1,719 5,380 4,817 9,470 Research and development 46,210 53,370 96,130 124,293 General and administrative 30,775 34,981 68,605 74,704 Restructuring charges — 3,566 — 8,032 Total operating expenses 78,704 97,297 169,552 216,499 Loss from operations ( 58,548 ) ( 58,163 ) ( 129,922 ) ( 139,135 ) Other income (expense): Interest income, net 3,232 6,083 6,828 12,164 Loss on equity method investment ( 4,673 ) — ( 4,673 ) — Gain (loss) on investments 1,987 ( 229 ) 773 ( 3,922 ) Other income (expense), net 809 ( 1,168 ) ( 6,338 ) ( 5,806 ) Total other income (expense) 1,355 4,686 ( 3,410 ) 2,436 Loss from continuing operations before income taxes ( 57,193 ) ( 53,477 ) ( 133,332 ) ( 136,699 ) Income tax (benefit) expense 128 ( 283 ) 48 ( 195 ) Net loss from continuing operations $ ( 57,321 ) $ ( 53,194 ) $ ( 133,380 ) $ ( 136,504 ) Net income (loss) from discontinued operations, net of tax 10,611 ( 7,106 ) 4,083 ( 14,753 ) Net loss $ ( 46,710 ) $ ( 60,300 ) $ ( 129,297 ) $ ( 151,257 ) Net income (loss) per share: From continuing operations $ ( 0.92 ) $ ( 0.97 ) $ ( 2.19 ) $ ( 2.50 ) From discontinued operations 0.17 ( 0.13 ) 0.06 ( 0.27 ) Total net loss per share $ ( 0.75 ) $ ( 1.10 ) $ ( 2.13 ) $ ( 2.77 ) Weighted average common shares outstanding: 62,094,356 54,858,982 60,835,896 54,552,006 Comprehensive loss: Net loss ( 46,710 ) ( 60,300 ) ( 129,297 ) ( 151,257 ) Other comprehensive (loss) income: Foreign currency translation adjustment ( 34 ) 2,586 ( 613 ) 3,435 Unrealized (loss) gain on available-for-sale securities ( 210 ) ( 83 ) ( 288 ) 24 Total other comprehensive (loss) income ( 244 ) 2,503 ( 901 ) 3,459 Comprehensive loss $ ( 46,954 ) $ ( 57,797 ) $ ( 130,198 ) $ ( 147,798 ) (1) Includes related party revenue of zero and $ 420 for the three months ended June 30, 2026 and 2025, respectively, and zero and $ 8,518 for the six months ended June 30, 2026 and 2025, respectively. The accompanying notes are an integral part of these condensed consolidated financial statements. 2 Table of Contents Ginkgo Bioworks Holdings, Inc. Condensed Consolidated Statements of Stockholders’ Equity (unaudited) (in thousands except share data) Three Months Ended June 30, 2026 Common Stock Shares Amount Additional Paid-In Capital Accumulated Deficit Accumulated Other Comprehensive Income Total Stockholders’ Equity Balance as of March 31, 2026 61,660,788 $ 6 $ 6,674,860 $ ( 6,232,907 ) $ 1,194 $ 443,153 Issuance of common stock upon exercise or vesting of equity awards 252,115 — — — — — Issuance of common stock in ATM offering, net of $ 560 issuance costs 1,798,199 — 16,489 — — 16,489 Stock-based compensation expense — — 7,596 — — 7,596 Other comprehensive income — — — — ( 244 ) ( 244 ) Net loss — — — ( 46,710 ) — ( 46,710 ) Balance as of June 30, 2026 63,711,102 $ 6 $ 6,698,945 $ ( 6,279,617 ) $ 950 $ 420,284 Six Months Ended June 30, 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 3,705,605 — — — — — Issuance of common stock in ATM offering, net of $ 560 issuance costs 1,798,199 — 16,489 — — 16,489 Stock-based compensation expense — — 25,403 — — 25,403 Other comprehensive income — — — — ( 901 ) ( 901 ) Net loss — — — ( 129,297 ) — ( 129,297 ) Balance as of June 30, 2026 63,711,102 $ 6 $ 6,698,945 $ ( 6,279,617 ) $ 950 $ 420,284 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 June 30, 2025 Common Stock Shares Amount Additional Paid-In Capital Accumulated Deficit Accumulated Other Comprehensive Income (Loss) Total Stockholders’ Equity Balance as of March 31, 2025 54,698,246 $ 5 $ 6,576,786 $ ( 5,928,514 ) $ ( 850 ) $ 647,427 Issuance of common stock upon exercise or vesting of equity awards 624,166 — — — — — Release of 6,647 common shares from escrow related to acquisition — — 298 — — 298 Issuance of common stock in settlement of purchase price holdback 102,922 1 776 — — 777 Stock-based compensation expense — — 22,247 — — 22,247 Other comprehensive income — — — — 2,503 2,503 Net loss — — — ( 60,300 ) — ( 60,300 ) Balance as of June 30, 2025 55,425,334 $ 6 $ 6,600,107 $ ( 5,988,814 ) $ 1,653 $ 612,952 Six Months Ended June 30, 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 956,627 — — — — — Release of 24,913 common shares from escrow related to acquisition — — 1,237 — — 1,237 Issuance of common stock in settlement of purchase price holdback 102,922 1 776 — — 777 Stock-based compensation expense — — 42,678 — — 42,678 Other comprehensive income — — — — 3,459 3,459 Net loss — — — ( 151,257 ) — ( 151,257 ) Balance as of June 30, 2025 55,425,334 $ 6 $ 6,600,107 $ ( 5,988,814 ) $ 1,653 $ 612,952 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) Six Months Ended June 30, 2026 2025 Cash flows from operating activities: Net loss $ ( 129,297 ) $ ( 151,257 ) Net income (loss) from discontinued operations, net of tax 4,083 ( 14,753 ) Net loss from continuing operations ( 133,380 ) ( 136,504 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 25,114 30,071 Stock-based compensation 23,448 36,189 (Gain) loss on investments ( 773 ) 3,958 Loss on equity method investment 4,673 — Change in fair value of notes receivable 6,759 5,285 Change in fair value of contingent consideration — ( 4,232 ) Non-cash lease expense 13,257 14,866 Accretion of discount on marketable securities ( 91 ) — Other non-cash activity ( 289 ) 46 Changes in operating assets and liabilities: Accounts receivable 3,471 2,198 Prepaid expenses and other current assets ( 775 ) ( 3,043 ) Operating lease right-of-use assets — 3,814 Other non-current assets 142 ( 125 ) Accounts payable, accrued expenses and other current liabilities ( 7,657 ) ( 3,341 ) Deferred revenue, current and non-current zero and $( 7,958 ) from related parties ( 5,638 ) ( 24,005 ) Operating lease liabilities, current and non-current ( 10,743 ) ( 11,638 ) Other non-current liabilities ( 6,124 ) 5,156 Net cash used in operating activities - continuing operations ( 88,606 ) ( 81,305 ) Net cash used in operating activities - discontinued operations ( 2,353 ) ( 10,470 ) Net cash used in operating activities ( 90,959 ) ( 91,775 ) Cash flows from investing activities: Purchases of marketable debt securities ( 127,445 ) ( 320,132 ) Maturities of marketable debt securities 166,168 64,958 Purchases of property and equipment ( 4,552 ) ( 7,660 ) Other 48 262 Net cash provided by (used in) investing activities 34,219 ( 262,572 ) Cash flows from financing activities: Proceeds from ATM offering 17,049 — Payment of issuance costs related to ATM offering ( 560 ) — Principal payments on finance leases ( 19 ) ( 305 ) Net cash provided by (used in) financing activities 16,470 ( 305 ) Effect of foreign exchange rates on cash and cash equivalents ( 86 ) 260 5 Table of Contents Net decrease in cash, cash equivalents and restricted cash ( 40,356 ) ( 354,392 ) 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 84,535 203,566 Restricted cash, end of period 87,480 47,785 Cash, cash equivalents and restricted cash, end of period $ 172,015 $ 251,351 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 its customers cell engineering tools for biological R&D, where Ginkgo enables its customers to conduct certain in-house R&D activities themselves. Ginkgo’s services and tools are designed to offer customers better results on the dimensions of probability of success, speed, or cost – and ideally on all three. Our Autonomous Lab is a flexible wet lab built from our Reconfigurable Automation Cart (“RAC”) systems capable of large-scale data generation; it powers generative AI and machine learning (“ML”) tools that enable more successful biological R&D. Discontinued Operations On April 3, 2026, the Company completed a divestiture of its Biosecurity business, which was previously reported as a separate segment, whereby Perimeter Systems, Inc. (the “Purchaser” or “Perimeter”) issued to the Company common equity of the Purchaser representing a minority interest in the Purchaser, in exchange for substantially all of the Company’s operations comprising its Biosecurity business (the “Biosecurity Divestiture”). Refer to Note 2 for additional details on the Biosecurity Divestiture. The Company is presenting the financial results of the Biosecurity business as discontinued operations for all periods presented within the accompanying condensed consolidated statements of operations and cash flows. The accompanying condensed consolidated balance sheet as of December 31, 2025 reflect the transferred Biosecurity assets as held for sale. Prior to the Biosecurity Divestiture, the Biosecurity business provided services to government customers who are working to identify, monitor, prevent, and mitigate biological threats. Basis of Presentation The accompanying condensed consolidated financial statements have been prepared in conformity with the rules and regulations of the SEC and generally accepted accounting principles in the United States (“GAAP”) for interim financial reporting. Accordingly, certain detailed disclosures which would normally be included with annual financial statements have been omitted. In the opinion of management, all normal recurring adjustments necessary for a fair presentation have been made. These condensed consolidated financial statements should be read in conjunction with the 2025 Annual Report. Interim results are not necessarily indicative of results for a full year. Principles of Consolidation The accompanying condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany accounts and transactions have been eliminated. Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, revenues and expenses, and the disclosure of contingent liabilities in the consolidated financial statements. The Company bases its estimates on historical experience and other market-specific or relevant assumptions that it believes to be reasonable under the circumstances. Reported amounts and disclosures reflect the overall economic conditions that management believes are most likely to occur, and the anticipated measures management intends to take. Actual results could differ materially from those estimates. All revisions to accounting estimates are recognized in the period in which the estimates are revised. 7 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) Significant Accounting Policies There have been no new or material changes to the Company’s significant accounting policies during the six months ended June 30, 2026 as compared to the significant accounting policies described in Note 2 to the Company’s 2025 consolidated financial statements included in the 2025 Annual Report. Recently Issued Accounting Pronouncements There were no new recently issued accounting pronouncements that are of significance or potential significance to the Company from those disclosed within Note 2 to the Company’s 2025 consolidated financial statements included in the 2025 Annual Report. 2. Discontinued Operations and Assets Held for Sale On February 26, 2026, Ginkgo Bioworks, Inc. (the “Seller”), a wholly owned subsidiary of the Company, entered into a Stock Purchase Agreement (the “Purchase Agreement”) with Tower Biosecurity, Inc., also known as Perimeter Systems, Inc. (the “Purchaser” or “Perimeter”), for the Biosecurity Divestiture. The transaction closed on April 3, 2026 (the “Closing Date”). Pursuant to the Purchase Agreement, the Seller contributed to the Purchaser all of the issued and outstanding equity interests of Ginkgo Biosecurity, LLC (“Biosecurity”), constituting substantially all of the Company's operations comprising its Biosecurity business. In exchange, the Purchaser issued to the Seller shares of its common stock representing approximately 20 % of the issued and outstanding equity of the Purchaser on a fully diluted basis. The Seller’s common equity interest in the Purchaser constituted approximately 44 % of the outstanding common equity of the Purchaser as of the Closing Date. Concurrently, the Company and Perimeter entered into a Transition Services Agreement (“TSA”) to ensure the continuity of business operations, pursuant to which the Company and Perimeter provide each other specified services on a temporary basis. The Seller provides certain services to the Purchaser, including, but not limited to, information technology access and support, certain scientific services, human resources, finance and accounting functions. The TSA is expected to conclude within 12 months of the Closing Date. The billings under the TSA are not expected to be significant. The Biosecurity Divestiture represents a strategic shift that has a major effect on the Company's operations and financial results. The Company no longer operates in the biosecurity market since the Closing Date. The Biosecurity Divestiture meets both the criteria to be classified as a discontinued operation. As such, the results of operations of the Biosecurity business are presented as a single line item, “Net income (loss) from discontinued operations, net of tax,”on the condensed consolidated statements of operations for all periods presented. All prior periods presented have been recast accordingly. Deconsolidation of the Biosecurity business occurred on the Closing Date. In connection with the deconsolidation, the Company recognized a net gain on deconsolidation of $ 24.5 million (net of the Company's equity interest contributed to Perimeter management) within in the second quarter of 2026. No cash consideration was received by the Company in connection with the Biosecurity Divestiture. The fair value of the retained equity interest in Perimeter of $ 12.3 million was determined using the Option Pricing Method (“OPM”) under a Black-Scholes framework (a Level 3 fair value measurement), which allocates equity value across Perimeter's capital structure based on the economics of each security class. Volatility was selected based on the historical equity volatility of a set of comparable guideline public companies and a discount for lack of marketability was applied. Following deconsolidation, the Company accounts for its retained approximately 44 % common equity interest in Perimeter using the equity method of accounting. The Company has the ability to exercise significant influence over the operating and financial policies of Perimeter through its common equity ownership and rights under the Stockholders Agreement. The Company will recognize its proportionate share of Perimeter's operation, equaling approximately 44 %. In connection with the Biosecurity Divestiture, approximately 30 % of Perimeter's equity was issued to Perimeter management previously employed by Ginkgo. In accordance with ASC 718 and ASC 710, the fair value of the Perimeter equity awarded to Perimeter management (approximately $ 15.4 million) was recognized as compensation expense in the second quarter of 2026. This amount is presented within discontinued operations on the Company’s condensed consolidated statements of operations. The management compensation tranche was measured at fair value on the Closing Date using the same Option Pricing Method applied to value the Company's common equity interest in Perimeter. 8 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) The following table presents the major components of the “Income (loss) from discontinued operations, net of tax” in the condensed consolidated statements of operations (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2026 2025 2026 2025 Revenue $ 1,464 $ 10,470 $ 7,674 $ 20,558 Costs and operating expenses: Cost of revenue — 9,442 5,352 17,399 General and administrative 15,360 8,298 23,061 17,618 Restructuring charges — 108 — 915 Total operating expenses 15,360 17,848 28,413 35,932 Loss from operations ( 13,896 ) ( 7,378 ) ( 20,739 ) ( 15,374 ) Gain on deconsolidation 24,507 — 24,507 — Other income — 272 315 621 Total other income 24,507 272 24,822 621 Income (loss) from discontinued operations $ 10,611 $ ( 7,106 ) $ 4,083 $ ( 14,753 ) The following table presents the major components of assets held for sale on the condensed consolidated balance sheet (in thousands): As of December 31, 2025 Property, plant and equipment, net $ 412 Intangible assets, net 3,442 Total assets held for sale $ 3,854 9 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) The following table presents the net cash used in discontinued operations in the condensed consolidated statements of cash flows (in thousands): Six Months Ended June 30, 2026 2025 Cash flows from operating activities: Income (loss) from discontinued operations $ 4,083 $ ( 14,753 ) Adjustments to reconcile net income (loss) from discontinued operations to net cash provided by (used in) operating activities - discontinued operations: Depreciation and amortization 561 1,088 Stock-based compensation 17,314 6,489 Gain on deconsolidation ( 24,507 ) — Changes in operating assets and liabilities: Accounts receivable 7,780 ( 2,610 ) Prepaid expenses and other current assets 558 771 Accounts payable, accrued expenses and other current liabilities ( 8,142 ) ( 1,784 ) Deferred revenue, current and non-current — 329 Net cash used in operating activities - discontinued operations $ ( 2,353 ) $ ( 10,470 ) There were no investing or financing cash flow activities for the discontinued operations in the six months ended June 30, 2026 or 2025, respectively. The table below provides a reconciliation of the beginning and ending balances for the Company's equity method investment in Perimeter for the six months ended June 30, 2026 (in thousands): Equity Method Investment Balance at January 1, 2026 $ — Addition 12,288 Loss on equity method investment ( 4,673 ) Balance at June 30, 2026 $ 7,615 3. Restructuring In the second quarter of 2024, in connection with the Company’s plans to reduce operational expenditures, management, with the approval of the Company’s Board of Directors, approved and commenced a restructuring plan. This plan included a reduction in labor expenses, primarily through a workforce reduction of more than 50 %, and the consolidation and subleasing of certain facilities. Initial workforce reductions commenced in June 2024 and substantially concluded by December 31, 2025. The Company plans to consolidate certain facilities through various actions, including combining office and laboratory operations into fewer locations, subleasing unused or underutilized facilities. While the Company has substantially completed the majority of its facility consolidation actions with excess space available for sublease, the subleasing of unused or underutilized facilities is expected to extend at least throughout 2026 and may not occur prior to termination of such lease, depending on market conditions. The Company is currently unable to estimate the costs associated with consolidating its facilities. These costs may include, but are not limited to, losses on subleases, contract terminations, asset impairments, sale or disposal of equipment or other long-lived assets, and related costs and fees pertaining to the consolidation, closure, or disposition of facilities. Additional charges may be incurred as the Company progresses its restructuring plan and such charges could be material. 10 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) The following table presents the change in the accrued liability balance related to the restructuring activities, which is included in “Accounts payable” and “Accrued expenses and other current liabilities” in the accompanying condensed consolidated balance sheets (in thousands): Employee Termination Costs and Other Liability balance at December 31, 2025 $ 2,601 Cash payments ( 2,601 ) Liability balance at June 30, 2026 $ — Restructuring charges were zero and $ 3.6 million during the three months ended June 30, 2026 and 2025, respectively. Restructuring charges were zero and $ 8.0 million during the six months ended June 30, 2026 and 2025, respectively. Restructuring charges consisted entirely of employee termination costs and other. 4. Fair Value Measurements The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis (in thousands): As of June 30, 2026 Total Level 1 Level 2 Level 3 Assets: Cash and cash equivalents: Money market funds $ 86,511 $ 86,511 $ — $ — U.S. Treasury securities 15,998 15,998 — — Corporate bonds 3,315 — 3,315 — Marketable securities: Commercial paper 916 — 916 — U.S. Treasury securities 126,210 126,210 — — Corporate bonds 70,784 — 70,784 — Marketable equity securities 19,718 19,718 — — Investments: Synlogic, Inc. warrants (1) 119 — 119 — Marketable equity securities 1,343 1,343 — — Total assets $ 324,914 $ 249,780 $ 75,134 $ — 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 11 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) As of 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 six months ended June 30, 2025, transfers into Level 3 consisted of a note receivable that was transferred from Level 2 to Level 3 upon a change in valuation technique. There were no other transfers between Levels 1, 2, or 3 during the six months ended June 30, 2026 or June 30, 2025. 12 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 six months ended June 30 (in thousands): Notes Receivable Contingent Consideration Balance at January 1, 2026 $ 7,126 $ 5,690 Change in fair value ( 7,126 ) — Balance at June 30, 2026 $ — $ 5,690 Balance at January 1, 2025 1,843 9,922 Additions 173 — Change in fair value 50 ( 4,232 ) Settlements and payments ( 50 ) — Conversion to preferred stock ( 1,463 ) — Transfers into Level 3 6,987 — Balance at June 30, 2025 $ 7,540 $ 5,690 Notes Receivable For all of its notes receivable, the Company has elected the fair value option, under which changes in fair value are recorded in other income (expense), net, in the condensed consolidated statements of operations and comprehensive loss. The Company holds a senior secured note in the original principal amount of $ 11.8 million issued by Bolt Threads, Inc. (“Bolt”), which bears interest at 12 % per annum, is due December 31, 2027, and is included in other non-current assets at its estimated fair value. During the six months ended June 30, 2026, Bolt disclosed it ceased operations. Any proceeds recovered from the Bolt note as the result of a potential disposition of Bolt assets are expected to be immaterial. As such, during the six months ended June 30, 2026, the Company reduced the carrying value of the senior secured note to zero. As of December 31, 2025, the Company used a discounted cash flow model to estimate the fair value of the senior secured note, incorporating significant unobservable inputs such as the recovery rate, a risk-adjusted discount rate, and a potential settlement scenario. The Company also held a series of convertible debt instruments issued by customers as payment for cell engineering services. The Company used a scenario-based method to value the convertible debt instruments. Under this method, future cash flows are evaluated under various payoff scenarios, probability-weighted, and discounted to present value. The significant unobservable (Level 3) inputs used in the fair value measurement as of December 31, 2025 included scenario probabilities ranging from 5 % to 45 %, a discount rate of 15.5 % and estimated time to event date of approximately one year . Significant changes in these inputs could have resulted in a significantly lower or higher fair value measurement. As of June 30, 2026, the Company’s convertible notes receivable had an unpaid principal balance of $ 7.5 million and a fair value of zero , compared to an unpaid principal balance of $ 9.7 million and a fair value of $ 0.5 million as of December 31, 2025. Contingent Consideration In connection with various business acquisitions, the Company is required to make contingent earnout payments payable upon the achievement of certain technical, commercial and/or performance milestones. The Company also issued restricted stock in connection with acquisitions, which is subject to vesting conditions and is classified as contingent consideration liability. 13 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 six months ended June 30, 2026 or 2025, respectively. The fair value of contingent consideration related to earnout payments from acquisitions was estimated using unobservable (Level 3) inputs as illustrated in the table below. The fair value of contingent consideration related to restricted stock was estimated using the quoted price of Ginkgo’s Class A common stock, an estimate of the number of shares expected to vest, probability of vesting, and a discount rate. Material increases or decreases in these inputs could result in a higher or lower fair value measurement. Changes in the fair value of contingent consideration are recorded in general and administrative expense in the condensed consolidated statements of operations and comprehensive loss. The following table provides quantitative information regarding Level 3 inputs used in the fair value measurements of contingent consideration liabilities as of the periods presented: June 30, 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 21.3 % 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 and six months ended June 30, 2026, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies. During the six months ended June 30, 2025, the Company recorded an impairment of $ 1.8 million related to an investment in the preferred stock of a privately held company after concluding that the investment had substantially no value. During the three months ended June 30, 2025, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies. No impairment losses related to Simple Agreements for Future Equity (“SAFEs”) were recorded during the three and six months ended June 30, 2026 or 2025, respectively. 14 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 June 30, 2026 Amortized Cost Unrealized Gains Unrealized Losses Fair Value U.S. Treasury securities $ 142,301 $ 7 $ ( 100 ) $ 142,208 Corporate bonds 74,170 12 ( 83 ) 74,099 Commercial paper 916 — — 916 Marketable equity securities — — — 19,718 Total cash equivalents and marketable securities 217,387 19 ( 183 ) 236,941 Less: cash equivalents ( 19,315 ) — 2 ( 19,313 ) Marketable securities $ 198,072 $ 19 $ ( 181 ) $ 217,628 As of 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 June 30, 2026, including $ 19.3 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands): Amortized cost Fair value Due within one year $ 169,607 $ 169,553 Due after one year through five years 47,777 47,670 6. Investments and Equity Method Investments The Company has partnered with other investors to form business ventures, including Motif FoodWorks, Inc. (“Motif”), Allonnia, LLC (“Allonnia”), Arcaea, LLC (“Arcaea”), Verb Biotics, LLC (“Verb Biotics”), BiomEdit, Inc. (“BiomEdit”), and Ayana Bio, LLC (“Ayana Bio”) (collectively “Platform Ventures”). The Company also partners with existing entities, including Genomatica and Synlogic, Inc. (“Synlogic”) (collectively, “Legacy Structured Partnerships”) with complementary assets for synthetic biology applications. The Company holds equity interests in these Platform Ventures and Legacy Structured Partnerships. The Company also holds equity interests in other public and private companies as a result of entering into collaboration and license revenue arrangements with these entities. Refer to Note 2 for additional details on the Company's equity method investment in Perimeter. The Company accounts for its investments in Platform Ventures under the equity method. Such investments had a carrying value of zero as of June 30, 2026 and December 31, 2025. The Company’s marketable equity securities consist of Synlogic common stock, Synlogic warrants and the shares of common stock of other publicly traded companies. Marketable equity 15 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) securities are measured at fair value with changes in fair value recorded in other income (expense) in the condensed consolidated statements of operations and comprehensive loss. The Company’s non-marketable equity securities consist of preferred stock of Genomatica and preferred and common stock of other privately held companies without readily determinable fair values. Non-marketable equity securities are initially recorded using the measurement alternative at cost and subsequently adjusted for any impairment and observable price changes in orderly transactions for the identical or a similar security of the same issuer. Impairment losses and adjustments from observable price changes are recorded in loss on investments in the condensed consolidated statements of operations and comprehensive loss. The Company also holds investments in early-stage synthetic biology product companies via SAFEs. The Company entered into SAFEs in conjunction with a revenue contract with a customer under which the Company grants the customer a prepaid cell engineering services credit equal to the principal amount of the SAFE (the “Purchase Amount”), which may be used and drawn down as payment for the Company’s research and development services. The SAFEs will automatically convert into shares of preferred stock equal to the Purchase Amount divided by the discount price, which is calculated as the price per share sold in a qualified equity financing multiplied by a discount rate. The SAFEs also provide the Company with the right to future equity of the entity in a liquidation scenario or the cash-out amount in liquidation and dissolution scenarios or at the election of the SAFE issuer prior to an agreed outside date. The Company initially records SAFEs at fair value (see Note 4 ) and adjusts the carrying amount of the instrument at each reporting period for any impairments. Investments consisted of the following (in thousands): As of June 30, 2026 As of December 31, 2025 SAFEs $ 2,188 $ 2,188 Non-marketable equity securities 11,125 11,125 Marketable equity securities 1,343 1,562 Synlogic warrants 119 191 Total $ 14,775 $ 15,066 The components of gain (loss) on investments for each period were as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2026 2025 2026 2025 Impairment charges $ — $ — $ — $ ( 1,844 ) Unrealized gains (losses) recognized on marketable equity securities and warrants 1,987 ( 229 ) 773 ( 2,078 ) Gain (loss) on investments $ 1,987 $ ( 229 ) $ 773 $ ( 3,922 ) The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of June 30, 2026, including cumulative unrealized losses, were as follows (in thousands): As of June 30, 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 Perimeter, Motif, Allonnia, Genomatica, Arcaea, BiomEdit, Verb Biotics, and Ayana Bio, the Company has concluded these entities represent variable interest entities (such entities, the “VIEs”). 16 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) While the Company has board representation on certain of these entities and is involved in the ongoing development activities of these entities via its participation on such entities’ joint steering committees (“JSC”), the Company has concluded that it is not the primary beneficiary of these entities because: (i) the Company does not control the board of directors of any of the VIEs, and no voting or consent agreements exist between the Company and other members of each respective board of directors or other investors, (ii) the holders of preferred security interests in the VIEs hold certain rights that require their consent prior to taking certain actions, which include certain significant operating and financing decisions, and (iii) the Company’s representation on the JSC of each respective entity does not give it control over the development activities of any of the VIEs, as all JSC decisions are made by consensus and there are no agreements in place that would require any of the entities to vote in alignment with the Company. As the Company’s involvement in the VIEs does not give it the power to control the decisions with respect to their development or other activities, which are their most significant activities, the Company has concluded that it is not the primary beneficiary of the VIEs. Additionally, the Company holds equity interests in certain privately-held companies that are not consolidated as the Company is not the primary beneficiary. As of June 30, 2026 and December 31, 2025, the maximum risk of loss related to the VIEs was limited to the carrying value of its investments in such entities. Refer to Note 6 for additional details on the Company’s investments and equity method investments. 8. Supplemental Financial Information Cash, Cash Equivalents and Restricted Cash The reconciliation of cash, cash equivalents and restricted cash reported within the condensed consolidated balance sheet to the totals shown within the condensed consolidated statements of cash flows is as follows (in thousands): As of June 30, 2026 2026 2025 Cash and cash equivalents $ 84,535 $ 203,566 Restricted cash included in prepaid expenses and other current assets (1) 2,915 10,949 Restricted cash and cash equivalents, non-current (2) 84,565 36,836 Total cash, cash equivalents and restricted cash $ 172,015 $ 251,351 (1) Includes primarily cash balances collateralizing letters of credit associated with the Company’s facility leases and customer prepayments requiring segregation and restrictions in its use in accordance with the customer agreement. (2) Includes primarily cash equivalents balances as of June 30, 2026 associated with a customer surety bond to fulfill its obligations under a contract with a U.S. Government National Laboratory and customer prepayments requiring segregation and restrictions in its use in accordance with the customer agreement. 17 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): Six Months Ended June 30, 2026 2025 Supplemental disclosure of non-cash investing and financing activities: Purchases of property and equipment included in accounts payable and accrued expenses $ 15 $ 35 Common stock issued for asset acquisitions — 777 Equity method investment retained upon deconsolidation of Biosecurity Business 12,288 — Property, Plant and Equipment, net Property, plant and equipment, net consisted of the following (in thousands): As of June 30, 2026 As of December 31, 2025 Lab equipment $ 142,605 $ 143,182 Leasehold improvements 138,317 140,513 Buildings and facilities 49,760 49,760 Construction in progress 4,950 192 Computer equipment and software 7,305 9,056 Furniture and fixtures 5,768 6,520 Land 6,060 6,060 Total property, plant and equipment 354,765 355,283 Less: Accumulated depreciation ( 197,580 ) ( 187,912 ) Property, plant and equipment, net $ 157,185 $ 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 June 30, 2026 Class A 10,500,000,000 55,202,925 52,322,106 Class B 4,500,000,000 8,957,129 8,388,996 Class C 800,000,000 3,000,000 3,000,000 15,800,000,000 67,160,054 63,711,102 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 18 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 June 30, 2026, the Company has issued 3.7 million shares of Class A common stock under the Sales Agreement for net proceeds of $ 34.6 million. 9. Intangible Assets, net Intangible assets, net consisted of the following (in thousands): Gross Carrying Value (1) Accumulated Amortization (1) Net Carrying Value Weighted Average Amortization Period (in Years) June 30, 2026: Developed technology $ 99,529 $ ( 55,142 ) $ 44,387 7.5 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 $ 4.1 million and $ 4.2 million for the three months ended June 30, 2026 and 2025, respectively, and $ 8.3 million and $ 8.4 million for the six months ended June 30, 2026 and 2025, respectively. As of June 30, 2026, estimated future amortization expense for identifiable intangible assets is as follows (in thousands): Remainder of 2026 $ 8,197 2027 10,216 2028 2,915 2029 2,915 2030 2,915 Thereafter 17,229 Total $ 44,387 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. 19 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 June 30, Six Months Ended June 30, 2026 2025 2026 2025 Research and development $ 4,822 $ 8,517 $ 12,845 $ 17,510 General and administrative 2,527 8,770 9,930 16,194 Cost of other revenue 246 1,516 673 2,485 Total $ 7,595 $ 18,803 $ 23,448 $ 36,189 The Company grants stock-based incentive awards pursuant to the 2021 Incentive Award Plan (the “2021 Plan”) and the 2022 Inducement Plan (the “2022 Inducement Plan”). As of June 30, 2026, there were 4,304,034 shares and 298,803 shares available for future issuance under the 2021 Plan and the 2022 Inducement Plan, respectively. Restricted Stock Units Restricted stock unit (“RSU”) awards granted before 2025 generally had a four-year requisite service period, with 25 % of the shares vesting on the first anniversary of the grant date and the remainder vesting monthly thereafter. RSU awards granted in March 2026 and after will vest in equal quarterly installments through January 2027. A summary of the RSU activity for the six months ended June 30, 2026 is presented below: Number of Shares Weighted Average Grant Date Fair Value Nonvested as of December 31, 2025 1,262,853 $ 55.07 Granted 704,507 7.20 Vested ( 598,188 ) 34.08 Forfeited ( 438,666 ) 46.67 Nonvested as of June 30, 2026 930,506 36.28 The weighted average grant date fair value of RSUs granted during the six months ended June 30, 2026 and June 30, 2025 was $ 7.20 and $ 7.95 , respectively. As of June 30, 2026, there was $ 27.6 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 1.4 years. Performance-based Restricted Stock Units In March 2025, the compensation committee of the Company's Board of Directors approved a grant of performance-based restricted stock unit (“PSU”) awards under the 2021 Plan to substantially all employees. The PSUs were eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2025 cash flow and bookings targets. PSU achievement percentages ranged from 49 % to 100 % of the award. The grant-date fair value of the PSUs was determined based on the closing price of the Company’s Class A common stock on the grant date. In March 2026, the compensation committee of the Company's Board of Directors approved a grant of PSU awards under the 2021 Plan to substantially all employees. The PSUs are eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2026 cash flow and bookings targets. Recipients must remain employed through the date the applicable vested shares are distributed, which is expected to occur in March 2027. PSU achievement percentages may range from zero to 100 % of the award. The grant-date fair value of the PSUs was determined based on the closing price of the Company’s Class A common stock on the grant date. 20 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) A summary of PSU activity for the six months ended June 30, 2026 is presented below: Number of Shares Weighted Average Grant Date Fair Value Nonvested as of December 31, 2025 4,407,287 $ 8.06 Granted 3,102,611 7.06 Vested ( 3,107,417 ) 8.04 Forfeited ( 1,852,377 ) 7.78 Nonvested as of June 30, 2026 2,550,104 7.06 As of June 30, 2026, there was $ 15.0 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately 0.8 years, assuming a 100 % PSU achievement rate. Actual expense recognized may vary based on the final achievement rate . 12. Revenue Recognition Disaggregation of Revenue The following table sets forth the percentage of revenues by industry based on total revenue: Three Months Ended June 30, Six Months Ended June 30, 2026 2025 2026 2025 Government and defense 45 % 21 % 41 % 19 % Pharmaceutical and biotechnology 20 44 29 38 Agriculture 20 23 16 32 Food and nutrition 7 6 7 5 Consumer and technology 6 2 3 1 Industrial and environment 2 4 4 5 Total revenue 100 % 100 % 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 six months ended June 30, 2026 and June 30, 2025, but continues to recognize non-cash revenue from prior contracts. Revenue recognized relating to non-cash consideration was $ 0.8 million and $ 1.2 million for the three months ended and June 30, 2026, and 2025 respectively, and $ 1.3 million and $ 9.9 million for the six months ended and June 30, 2026, and 2025 respectively. The Company’s total revenue is primarily generated from customers located in the United States. For the three months ended months ended June 30, 2026 and 2025, U.S. customers accounted for 83 % and 79 %, respectively. For the six months ended June 30, 2026 and 2025, U.S. customers accounted for 74 % and 80 %, respectively. For the six months ended June 30, 2026 and 2025, customers from Denmark accounted for 11 % and 11 %, respectively. Contract Balances The Company recognizes a contract asset when the Company transfers goods or services to a customer before the customer pays consideration or before payment is due, excluding any amounts presented as accounts receivable. The Company had no contract asset balances as of June 30, 2026 and December 31, 2025. The Company’s accounts receivable consists of both billed and unbilled amounts. Unbilled receivables arise when revenue is recognized in excess of invoiced amounts and represent the Company’s unconditional right to consideration for goods or services already transferred to the customer. The 21 Table of Contents Ginkgo Bioworks Holdings, Inc. Notes to Condensed Consolidated Financial Statements (unaudited) balance of unbilled accounts receivable, included in accounts receivable, net in the accompanying condensed consolidated balance sheets, was $ 7.4 million and $ 14.5 million as of June 30, 2026 and December 31, 2025, respectively. Contract liabilities, or deferred revenue, primarily consist of payments received in advance of performance under the contract or when the Company has an unconditional right to consideration under the terms of the contract before it transfers goods or services to the customer. The Company’s collaborative arrangements with its investees and related parties typically include upfront payments consisting of cash or non-cash consideration for future research and development services and non-cash consideration in the form of convertible financial instruments and equity securities for licenses that will be transferred in the future. The Company records the upfront cash payments and fair value of the convertible financial instruments and equity securities as deferred revenue. The Company also invoices customers based on contractual billing schedules, which results in the recording of deferred revenue to the extent payment is received prior to the Company’s performance of the related services. Contract liabilities are recognized as revenue as (or when) the Company performs under the contract. During the six months ended June 30, 2026, the Company recognized $ 13.4 million of revenue that was included in the contract liabilities balance of $ 94.1 million as of December 31, 2025. During the six months ended June 30, 2025, the Company recognized $ 35.6 million of revenue that was included in the contract liabilities balance of $ 126.5 million as of December 31, 2024. Performance Obligations The aggregate amount of the transaction price that was allocated to performance obligations that have not yet been satisfied or are partially satisfied as of June 30, 2026 and December 31, 2025 was $ 113.0 million and $ 136.8 million, respectively. The Company has elected the practical expedient not to provide the remaining performance obligation disclosures related to contracts for which the Company recognizes revenue on a cost-plus basis in the amount to which it has the right to invoice. As of June 30, 2026, approximately $ 8.9 million of the unsatisfied or partially satisfied performance obligations is expected to be recognized as revenue in 2026, based on the projected customer program end dates; $ 35.2 million between 2026 and 2027; $ 61.6 million between 2026 and 2028; $ 3.4 million between 2026 and 2029; and $ 3.9 million between 2026 and 2030. 13. Segment Information As a result of the Biosecurity Divestiture (Note 2 ), the Company manages its operations as a single operating and reportable segment. This structure reflects the Company’s internal management framework and the approach its Chief Operating Decision Maker (“CODM”) uses to evaluate operating results and allocate resources. The Company’s reportable segment is that for which discrete financial information is available and whose results are regularly provided to the Company’s CODM, consisting of the Chief Executive Officer and the President, for the purpose of allocating resources and assessing financial performance. The CODM evaluates the financial performance of the Company’s segment based on loss from continuing operations before income taxes. The CODM is primarily provided with loss from continuing operations before income taxes on a quarterly basis, as well as during the annual budgeting and forecasting process, and uses this information to monitor the Company’s performance, including budget-to-actual results, and to make decisions about the allocation of operating and capital resources. The Company has determined its significant segment expenses are cost of revenue, research and development expenses, and general and administrative expenses (exclusive of certain costs and expenses), which are regularly provided to the CODM. The CODM is not provided with asset information; therefore, such information is not presented. The accounting policies used to prepare the reportable segments financial information are the same as those used to prepare the Company’s consolidated financial statements. The classification of costs differs from the presentation in the condensed consolidated statement of operations as described below. 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 June 30, Six Months Ended June 30, 2026 2025 2026 2025 Cell Engineering Revenue $ 20,156 $ 39,134 $ 39,630 $ 77,364 Costs and operating expenses: Cost of other revenue (1) 1,472 3,865 4,144 6,986 Research and development (1) 30,433 31,065 60,538 79,735 General and administrative (1) 11,108 15,986 23,831 35,639 Stock-based compensation (2) 8,037 18,770 24,745 36,483 Depreciation and amortization 12,315 15,249 25,114 30,071 Restructuring charges (3) — 3,566 — 8,032 Carrying cost of excess space (net of sublease income) (4) 14,233 12,413 30,074 24,088 Merger and acquisition related expense (income) (5) 1,106 ( 3,617 ) 1,106 ( 4,535 ) Other (income) expense, net (6) ( 1,355 ) ( 4,686 ) 3,410 ( 2,436 ) Loss from continuing operations before income taxes $ ( 57,193 ) $ ( 53,477 ) $ ( 133,332 ) $ ( 136,699 ) (1) The costs and operating expenses exclude expenses which are separately captioned below. (2) Includes $ 0.4 million and $ 0.2 million in employer payroll taxes for three months ended June 30, 2026 and 2025, respectively, and $ 1.3 million and $ 0.5 million for six months ended June 30, 2026 and 2025, respectively. (3) See Note 3 , Restructuring, for composition of costs. (4) The carrying cost of excess space includes base rent, common area maintenance charges, and real estate taxes associated with facilities the Company is not occupying, net of any sublease income from these spaces. (5) Represents transaction and integration costs directly related to mergers, acquisitions, and divestitures, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) securities litigation costs. (6) Includes interest income, interest expense, loss on investments, changes in fair value of certain assets and liabilities, and other gains and losses. 14. Net Loss per Share The following potential common shares, presented based on amounts outstanding at each period end, were excluded from the calculation of diluted net loss per share for the periods presented because including them would have been anti-dilutive: As of June 30, 2026 2025 Unvested PSUs 2,550,104 4,951,489 Unvested RSUs 930,506 2,496,161 Earnout shares (1) 3,793,063 3,793,534 Warrants to purchase Class A common stock 1,295,622 1,295,622 Outstanding stock options 343,650 433,187 8,912,945 12,969,993 (1) Represents employee and non-employee earnout shares for which the service-based and/or market-based vesting conditions have not been satisfied. 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 June 30, 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 June 30, Six Months Ended June 30, 2025 2025 Revenue: Genomatica $ 78 $ 352 Ayana Bio 342 582 Allonnia — 1 BiomEdit — 7,583 $ 420 $ 8,518 During the three and six months ended June 30, 2026, the Company recognized zero revenue from related parties. Refer to Note 6 for additional details on the Company’s investments and equity method investments held in its related parties. 24 Table of Contents