Ginkgo Bioworks Holdings, Inc. 10-Q

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations. The following discussion and analysis of our financial condition and results of operations should be read in conjunction with the unaudited condensed consolidated financial statements and related notes thereto included elsewhere in this Quarterly Report on Form 10-Q. This discussion contains forward-looking statements that reflect our plans, estimates and beliefs that involve risks and uncertainties. Actual results may differ materially from those anticipated in these forward-looking statements as a result of many factors, including those discussed in Item 1A “Risk Factors” and “Cautionary Note Regarding Forward-Looking Statements” elsewhere in this Quarterly Report on Form 10-Q and in our 2024 Annual Report. Overview Our mission is to make biology easier to engineer. Ginkgo sells services in two business segments: cell engineering , where we provide biological research and development (“R&D”) services for our customers across a range of industries, and biosecurity , where we provide services to government and commercial customers so they can work to identify, monitor, prevent, mitigate, and ultimately protect humanity from biological threats. Cell Engineering Ginkgo does not make end products; instead, we offer biological R&D services on our platform to enable our customers to bring their products to market. Historically, Ginkgo’s primary service offering has been end-to-end cell engineering R&D services ( solutions ). In 2024, Ginkgo expanded its service offering to also include services that provide our customers cell engineering tools for biological R&D, which are intended to provide more targeted and bespoke resources to customers that continue to conduct in-house R&D. Compounding and mutually reinforcing improvements of our laboratory automation and software infrastructure—our Foundry—and our reusable data assets—our Codebase—enable us to improve our services with each successive project. • Our Foundry is a flexible capability for large scale data generation; it powers generative artificial intelligence (“AI”) and machine learning tools that enable more successful biological R&D. We now offer services providing such data generation and automation tools directly to Ginkgo customers. • Our Codebase is a data asset comprising best practices for cell engineering, along with sequences and host cells that have been honed through dozens of programs and can be directly reusable for our end-to-end cell engineering solutions. Our end-to-end cell engineering solutions are typically scoped and delivered as a program ranging in duration from several months to several years. A typical deliverable for the program would comprise an engineered strain or cell line and an associated bioprocess. For each of these programs, we generate economic value in two primary ways. First, we charge usage fees for services, in much the same way that cloud computing companies charge usage fees for utilization of computing capacity or contract research organizations charge for services. Additionally, we have historically negotiated a value share with our customers (in the form of royalties, milestones, and/or equity interests) in order to align our economics with the success of the programs enabled by our platform. Commencing in the second quarter of 2024, we announced changes in prospective commercial terms, including the removal of downstream value share from certain program types. We charge customers fees for the services we provide in our cell engineering tools offerings. Typically, these fees are structured as a fixed fee for a fixed scope of work. Fees for our data generation products (“Datapoints”), which provide large, biological datasets for customers to train their AI models, synthesizing and testing the output of customer existing models, and generating datasets for lead selection, hit selection, or a variety of other data science applications, are typically earned over a shorter period of time (weeks to months) than for end-to-end cell engineering solutions which may be multi-year programs. Fees for our automation solutions are typically earned over a period that covers design, build, and deployment and range from six to twelve months. In addition, we offer support services with fixed fees covering the support periods. 32 Table of Contents A selection of our cell engineering tools offerings are described below. Datapoints Recent advances in machine-learning (ML), molecular simulation, and other computational techniques hold great promise to improve our ability to program cells. We believe our Foundry is well-positioned to build the kind of large, well-structured datasets that such computational approaches need to succeed. In time, we believe computational approaches will reduce the need for certain kinds of experiments (for example, we already use ML to make protein and enzyme design projects more efficient). To this end, we have introduced two new data generation services to provide high-quality data at the scale, price, and speed that AI-powered drug development demands: • Our Functional Genomics Datapoints services generate large, high fidelity transcriptomic and phenotypic datasets in the disease context of our customers’ choice to power AI models of cell and disease biology for use in target identification, target validation, and drug discovery; and • Our Antibody Developability Datapoints services generate biophysical antibody characterization developability datasets for our customers to use in AI model training and validation. Reconfigurable Automation Cart (“RAC”) Systems Ginkgo Automation’s capabilities build on years of internal expertise, encompassing hardware design, software integration, and applications development, epitomized in our offering of RACs: our Reconfigurable Automation Cart systems. The modularity and flexibility of the RACs enables high walkway time, high uptime, and high throughput experimentation for high-mix biological workflows like the kinds performed in Ginkgo’s Foundry and in our partners’ labs. In addition to providing advanced automation hardware and software, Ginkgo Automation’s deployments to third party customers include access to Catalyst Flow, a fully remote, active error resolution and troubleshooting support service. Catalyst Flow’s proactive monitoring is expected to enable Ginkgo’s scientists and engineers to identify and resolve approximately 80-90% of system errors remotely, without the need for our customers to initiate tickets. Biosecurity With a mission to make biology easier to engineer, we have always recognized the need to invest in biosecurity as a key component of our platform. We are building the future bioeconomy with our customers and partners, and we envision the future of biosecurity as a global immune system equipped with the capabilities to rapidly and reliably identify, monitor, prevent, and mitigate biological threats. The first, critical step in realizing this future is to build a robust early warning system for biological threats—this is the primary focus of Ginkgo’s Biosecurity business. Our primary biosecurity customers are governments. We currently provide biosecurity services via two core offerings as introduced in early 2024: • Canopy, which helps our customers generate high value genomic data from strategically positioned nodes (like airports and border checkpoints) via end-to-end biomonitoring programs; and • Horizon, our digital surveillance, analytics and insights platform that detects and monitors biothreats worldwide. Generating Economic Value Through Cell Programs Our cell engineering platform is a key enabling technology and source of intellectual property for our customers’ products. We earn Cell Engineering revenue for our R&D services. For each of our end-to-end cell engineering programs, we charge customers fees for the services we provide, typically structured as fixed fees, although we also have cost reimbursement arrangements. Additionally, we have historically negotiated a value share with our customers (in the form of royalties, milestones, and/or equity interests) in order to align our economics with the success of the programs enabled by our platform. Commencing in the second quarter of 2024, we announced changes in prospective commercial terms, including the removal of downstream value share from certain program types. 33 Table of Contents We charge customers fees for the services we provide in our cell engineering tools offerings. Typically, these fees are structured as a fixed fee for a fixed scope of work. Fees for our data generation products (“Datapoints”), which provide large, biological datasets for customers to train their AI models, synthesizing and testing the output of customer existing models, and generating datasets for lead selection, hit selection, or a variety of other data science applications, are typically earned over a shorter period of time (weeks to months) than for end-to-end cell engineering solutions which may be multi-year programs. Fees for our automation solutions are typically earned over a period that covers design, build, and deployment and range from six to twelve months. In addition, we offer support services with fixed fees covering the support periods. We typically structure customer contracts for Cell Engineering services to include one or more of the following: • upfront payments upon execution of an agreement or other fixed payments, which are generally recognized over the period of performance; • reimbursement of costs incurred for R&D services; • milestone payments upon achievement of specified technical criteria; and • downstream value share payments for certain program types. We have legacy customer arrangements, entered into prior to 2024, under which we may continue to provide services. These arrangements may include a combination of cash and/or non-cash consideration, as well as, when applicable, downstream value share payments which may take one or more of the following forms: • milestone payments, which may comprise cash and/or non-cash consideration upon the achievement of specified commercial criteria; • royalties on sales of products from or comprising engineered organisms; and • royalties related to cost of goods sold reductions realized by our customers. Our legacy customer arrangements offered flexible commercial terms on the service fees including the ability to pay a portion or all of such upfront fees in the form of non-cash consideration (convertible financial instruments and/or equity securities). Customer arrangements which involve non-cash consideration generally fall into two categories: Platform Ventures and Structured Partnerships. For a full description of these arrangements, refer to the Overview section of Management’s Discussion and Analysis of Financial Condition and Results of Operations, included in Part II, Item 7 of our 2024 Annual Report. Components of Results of Operations Revenue Cell Engineering Revenue We generate Cell Engineering revenue primarily through license and collaboration agreements, under which customers obtain rights to our proprietary technology and intellectual property for use in the development and commercialization of engineered organisms and derived products. Under these agreements, we typically provide R&D services for cell programming with the goal of producing an engineered cell that meets a mutually agreed specification. Our customers obtain license rights to the output of our services, which are primarily the optimized strains or cell lines, in order to manufacture and commercialize products derived from that licensed strain or cell line. Generally, the terms of these agreements provide that we receive some combination of: (1) service fees in the form of (i) upfront payments upon consummation of the agreement or other fixed payments, (ii) reimbursement for costs incurred for R&D services and (iii) milestone payments upon the achievement of specified technical criteria, plus (2) downstream value share payments in the form of (i) milestone payments upon the achievement of specified commercial criteria, (ii) royalties on sales of products from or comprising engineered organisms arising from the collaboration or licensing agreement and/or (iii) royalties related to cost of goods sold reductions realized by our customers. Royalties did not comprise a material amount of our revenue during any of the periods presented. Beginning in the second quarter of 2024, we announced changes to the commercial terms applicable to some new customer contracts, including revised intellectual property terms more favorable to customers and, in many cases, the removal of downstream value share from certain program types. 34 Table of Contents In the third quarter of 2024, we launched new cell engineering tools offerings, including Datapoints and lab automation solutions. Datapoints’ data generation products provide large, biological datasets for customers to train their AI models, synthesizing and testing the output of customer existing models, and generating datasets for lead selection, hit selection, or a variety of other data science applications. Our lab automation solutions combine modular hardware, control software and managed support to provide customers the ability to automate their own lab workflows in house. Cell Engineering revenue includes transactions with Platform Ventures and Legacy Structured Partnerships where, as part of these transactions, we received an equity interest in such entities. Specifically related to the Platform Ventures, in these transactions, we received upfront non-cash consideration in the form of common equity interests in these entities, while the Platform Ventures each received cash equity investments from strategic partners and financial investors. We view the upfront non-cash consideration as prepayments for licenses which will be granted in the future as we complete mutually agreed upon technical development plans. In these instances, we also receive cash consideration for the R&D services performed by us on a fixed fee or cost-plus basis. We are not compensated through additional milestone or royalty payments under these arrangements. Our transactions with Genomatica and Synlogic included the purchase of equity securities and the provision of R&D services. As we perform R&D services under the mutually agreed upon development plans, we recognize a reduction in the prefunded obligation on a cost-plus basis. These arrangements are further described in Notes 6 , 7 , and 15 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q. Cell Engineering revenue also includes transactions with early stage synthetic biology product companies where, as part of these transactions, we received upfront non-cash consideration in the form of current equity interests or financial instruments that are convertible into equity upon a triggering event. We issued the customer a prepaid cell engineering services credit in exchange for the upfront non-cash consideration, which can and has been drawn down as payment for R&D services performed under mutually agreed upon development plans. Downstream value share in the form of equity interest appreciation is not recognized as revenue but is expected to contribute to future cash flows upon liquidation, the amount and timing of which is inherently unpredictable. The initial fair value of the equity interests received may also decrease after contract inception and the amount of cash proceeds eventually realized may be less than the revenue recognized. Equity investments are accounted for under the equity method, the cost method, or are carried at fair value. Biosecurity Revenue We offer biosecurity services through our two core offerings: Canopy and Horizon. We are currently offering biomonitoring and bioinformatics support services domestically through our partnerships with the U.S. Centers for Disease Control and Prevention and XpresCheck, and internationally through our international programs. We are also engaged in a series of smaller partnerships that generate revenues through biosecurity services and R&D. We generate revenue through the sale of our end-to-end biomonitoring and bioinformatics support services. These offerings typically include, but are not limited to, sample collection, sample storage and transportation, outsourced laboratory analysis, access to results via a web-based portal, analytical reporting, and overall program management. In general, our agreements specify that we are entitled to compensation as services are performed. The timing of revenue recognition depends on the identified performance obligations but is generally recognized over time or as results are delivered to the customer. Costs and Operating Expenses Cost of Biosecurity Revenue The cost of Biosecurity revenue consists of costs related to our biomonitoring and bioinformatics support services. This includes costs incurred for sample collection equipment and materials, outsourced laboratory analysis, access to results reported through our proprietary web-based portal, and reporting of results to government and non-government customers. Additionally, the cost of Biosecurity revenue includes direct labor cost associated with bioinformatics, lab network management, delivery logistics, and customer support. 35 Table of Contents Cost of Other Revenue Cost of other revenue consists of costs related to our cell engineering tools offerings, including Datapoints and lab automation solutions. Such costs primarily include hardware, software, materials and labor. Research and Development Expenses The nature of our business, and primary focus of our activities, generates a significant amount of R&D expenses. R&D expenses represent costs incurred by us for the following: • development, operation, expansion and enhancement of our Foundry and Codebase; • costs incurred to deliver our end-to-end cell engineering solutions offering to customers; and • development of new offerings. The activities above incur the following expenses: • personnel compensation and benefits; • rent, facilities, depreciation, software, professional fees and other direct and allocated overhead expenses; and • laboratory supplies, consumables and related services provided under agreements with third parties and in-licensing arrangements. We expense R&D costs as incurred. Our R&D expenses were lower in the first half of 2025 compared to the first half of 2024, primarily due to our restructuring plan announced and commenced in the second quarter of 2024 as we rationalize our current development programs and prioritize our investments in our Foundry, Codebase and cell engineering tools offerings. We expect that our R&D expenses will either remain consistent or decline in 2025 as compared to 2024, reflecting the stabilization of our operational overhead and the impact of our restructuring actions. However, our R&D expenses could increase in 2025 due to employee incentive programs offered or additional costs and expenses arising from these restructuring actions. The nature, timing, and estimated costs required to support our growth will be dependent on advances in technology, our ability to attract new customers, and the rate of market penetration within our existing customer industries. General and Administrative Expenses General and administrative (“G&A”) expenses consist primarily of costs for personnel in executive, business development, finance, human resources, legal and other corporate administrative functions. G&A expenses also include professional legal services fees and costs incurred relating to litigation, corporate, intellectual property and patent matters, professional fees incurred for accounting, auditing, tax and administrative consulting services, insurance costs, facility-related costs not otherwise included in R&D expenses, and asset impairments. Our G&A expenses were lower in the first half of 2025 compared to the first half of 2024, primarily due to our restructuring plan announced and commenced in the second quarter of 2024, as we began reducing our operational overhead. We expect that our G&A expenses will either remain consistent or decline in 2025 as compared to 2024, reflecting the stabilization of our operational overhead and the impact of our restructuring actions. However, our G&A expenses could increase in 2025 due to employee incentive programs offered or additional costs and expenses arising from these restructuring actions. Conversely, we intend to maintain a strategic and opportunistic approach regarding inorganic G&A expenses arising from mergers, acquisitions, and other inorganic growth initiatives. Goodwill Impairment In the second quarter of 2024, due to a sustained decrease in the market price of our Class A common stock and overall market capitalization, we identified a goodwill impairment indicator related to our Cell Engineering reporting unit. We performed an interim impairment test, which resulted in a full impairment of the goodwill balance. 36 Table of Contents Restructuring Charges Restructuring charges are related to our restructuring plan, which was announced and commenced in the second quarter of 2024. These charges primarily include severance and other employee termination costs from a reduction in force that commenced in June 2024, as well as the impairment of a right-of-use asset due to the subleasing of a facility as part of real estate consolidation. Reductions in force are expected to be substantially completed in 2025, subject to compliance with applicable laws. While we have substantially completed the majority of our facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities is expected to extend into 2026 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. Additional details are included in Note 3 , Restructuring, of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q. Interest Income, Net Interest income, net consists primarily of interest earned on our cash and cash equivalents and marketable debt securities. Loss on Investments Loss on investments includes the change in fair value of our marketable equity securities in publicly traded companies and impairment losses recognized on non-marketable equity securities in privately held companies. Loss on Deconsolidation of Subsidiary Loss on deconsolidation of subsidiary pertains to our deconsolidation of our former foreign subsidiary Altar SAS (“Altar”) in the third quarter of 2024 as a result of a sale. Change in Fair Value of Warrant Liabilities The change in fair value of warrant liabilities reflects adjustments to the fair value of private placement warrants (“Private Placement Warrants”) and warrants formerly publicly traded on the NYSE. These warrants, classified as liabilities, were assumed as part of our merger with Soaring Eagle Acquisition Corp. (“SRNG”) on September 16, 2021, and were initially issued in connection with SRNG’s initial public offering. Warrant liabilities are remeasured at fair value at each balance sheet date and have substantially no value as of September 30, 2025. Other Income (Expense), Net Other income (expense), net primarily consists of changes in the fair value of notes receivable that we elected to account for under the fair value option and sublease rent income for the comparative periods in 2024. Provision for Income Taxes Income taxes are recorded in accordance with ASC 740 , Income Taxes , which provides for deferred taxes using an asset and liability approach. We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in our financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the financial statement and tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. A valuation allowance against deferred tax assets is recorded if, based on the weight of the available evidence, it is more likely than not that some or all the deferred tax assets will not be realized. For all periods presented, we have recorded a valuation allowance against the deferred tax assets that are not expected to be realized. We account for uncertain tax positions using a more-likely-than-not threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors, including, but not limited to, changes in the law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. Income taxes are determined at the applicable tax rates adjusted for non-deductible expenses, R&D tax credits and other permanent differences. Our income tax provision may be affected by changes to our estimates. 37 Table of Contents Results of Operations Comparison of the Three and Nine Months Ended September 30, 2025 and 2024 The following table presents our result of operations for the periods indicated: Three Months Ended September 30, Nine Months Ended September 30, (in thousands) 2025 2024 Change 2025 2024 Change Cell Engineering revenue $ 29,380 $ 75,089 $ (45,709) $ 106,744 $ 139,183 $ (32,439) Biosecurity revenue 9,457 13,957 (4,500) 30,015 44,013 (13,998) Total revenue 38,837 89,046 (50,209) 136,759 183,196 (46,437) Costs and operating expenses: Cost of Biosecurity revenue (1) 8,177 9,987 (1,810) 25,576 30,996 (5,420) Cost of other revenue (1) 4,625 2,016 2,609 14,095 3,930 10,165 Research and development (1) 69,353 77,006 (7,653) 193,646 347,684 (154,038) General and administrative (1) 44,954 52,292 (7,338) 137,276 188,864 (51,588) Goodwill impairment — — — — 47,858 (47,858) Restructuring charges 1,745 2,949 (1,204) 10,692 20,015 (9,323) Total operating expenses 128,854 144,250 (15,396) 381,285 639,347 (258,062) Loss from operations (90,017) (55,204) (34,813) (244,526) (456,151) 211,625 Other income (expense): Interest income, net 5,742 9,251 (3,509) 17,906 31,275 (13,369) Gain (loss) on investments 3,684 (6,912) 10,596 (238) (16,282) 16,044 Loss on deconsolidation of subsidiary — (7,013) 7,013 — (7,013) 7,013 Change in fair value of warrant liabilities — 1,528 (1,528) — 5,701 (5,701) Other income (expense), net (163) 1,572 (1,735) (5,348) 2,821 (8,169) Total other income (expense) 9,263 (1,574) 10,837 12,320 16,502 (4,182) Loss before income taxes (80,754) (56,778) (23,976) (232,206) (439,649) 207,443 Income tax (benefit) expense 1 (375) 376 (194) (154) (40) Net loss $ (80,755) $ (56,403) $ (24,352) $ (232,012) $ (439,495) $ 207,483 (1) Total stock-based compensation expense, inclusive of employer payroll taxes, was allocated as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Research and development $ 6,349 $ 3,214 $ 24,189 $ 48,028 General and administrative 9,590 10,799 30,998 46,608 Cost of Biosecurity revenue 534 — 2,127 — Cost of other revenue 1,630 — 4,115 — Total $ 18,103 $ 14,013 $ 61,429 $ 94,636 Cell Engineering Revenue Cell Engineering revenue was $29.4 million for the three months ended September 30, 2025, compared to $75.1 million for the three months ended September 30, 2024, a decrease of $45.7 million. This decrease was primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024. Cell Engineering revenue was $106.7 million for the nine months ended September 30, 2025, compared to $139.2 million for the nine months ended September 30, 2024, a decrease of $32.4 million. This decrease was primarily due to the 38 Table of Contents recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024, the recognition of $4.5 million in non-cash revenue from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024, and decreases in revenue for certain programs with customers in the industrial biotechnology industry. These decreases were partially offset by the recognition of $7.5 million in non-cash revenue from the release of a deferred revenue balance associated with the terminated BiomEdit, Inc. (“BiomEdit”) contract in the first quarter of 2025 (see Note 15 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q) and an increase in revenue related to programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries and with the U.S. government (healthcare and defense sectors). As discussed above in Components of Results of Operations, Cell Engineering revenue comprises both cash and non-cash consideration. Cell Engineering revenue recognized relating to non-cash consideration decreased from $48.0 million for the three months ended September 30, 2024 to zero for the three months ended September 30, 2025, and from $60.1 million for the nine months ended September 30, 2024 to $9.9 million for the nine months ended September 30, 2025, primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024, and the recognition of $4.5 million from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024, offset by the recognition of $7.5 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated BiomEdit contract in the first quarter of 2025. Biosecurity Revenue Biosecurity revenue was $9.5 million for the three months ended September 30, 2025, compared to $14.0 million for the three months ended September 30, 2024, a decrease of $4.5 million. This decrease was primarily due to lower revenue related to programs with the U.S. government and a foreign government. Biosecurity revenue was $30.0 million for the nine months ended September 30, 2025, compared to $44.0 million for the nine months ended September 30, 2024, a decrease of $14.0 million. This decrease was primarily due to lower revenue related to a programs with the U.S. government and a foreign government. Cost of Biosecurity Revenue The cost of Biosecurity revenue was $8.2 million for the three months ended September 30, 2025, compared to $10.0 million for the three months ended September 30, 2024, a decrease of $1.8 million. This decrease was primarily due to cost reductions implemented during 2025 as well as a reduction in activities supporting a program with the U.S. government. The cost of Biosecurity revenue was $25.6 million for the nine months ended September 30, 2025, compared to $31.0 million for the nine months ended September 30, 2024, a decrease of $5.4 million. This decrease was primarily due to cost reductions implemented during 2025 as well as a reduction in activities supporting a program with the U.S. government. Cost of Other Revenue The cost of other revenue was $4.6 million for the three months ended September 30, 2025, compared to $2.0 million for the three months ended September 30, 2024, an increase of $2.6 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which commenced in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses. The cost of other revenue was $14.1 million for the nine months ended September 30, 2025, compared to $3.9 million for the nine months ended September 30, 2024, an increase of $10.2 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which commenced in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses. Research and Development Expenses Our research and development expenses principally relate to the development of new offerings and the operation, expansion and enhancement of our existing service offerings utilizing our proprietary platform, which includes our Foundry and Codebase assets, to our cell engineering customers. Research personnel costs, including stock-based compensation, is our largest expense, totaling $19.3 million and $31.2 million for the three months ended September 30, 2025 and 2024, respectively, and $73.3 million and $152.5 million for the nine months ended September 30, 2025 and 39 Table of Contents 2024, respectively. We also acquired and expensed in-process research and development primarily through the issuance of our equity, aggregating to zero for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 2025 and 2024, respectively. Our remaining research and development costs are comprised primarily of rent and related facilities costs, information technology costs, depreciation pertaining to facilities and equipment, laboratory consumables, contract services, and routine costs and fees. Research and development expenses were $69.4 million for the three months ended September 30, 2025, compared to $77.0 million for the three months ended September 30, 2024, a decrease of $7.7 million. This decrease was primarily driven by reductions of $15.0 million in personnel-related compensation and benefits expenses, $8.0 million in rent and facilities expenses, $4.4 million in depreciation and amortization, $2.2 million in laboratory supplies, $2.0 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), $1.1 million in temporary labor and contractors, and $0.6 million in other operating expenses. These decreases were partially offset by an increase of $22.5 million in information technology expenses primarily due to a shortfall in contractually committed spending related to our strategic cloud and AI partnership with Google Cloud (see Note 10 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q) and $3.1 million in stock-based compensation expense (inclusive of employer payroll taxes). Research and development expenses were $193.6 million for the nine months ended September 30, 2025, compared to $347.7 million for the nine months ended September 30, 2024, a decrease of $154.0 million. This decrease was primarily driven by reductions of $54.6 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $30.3 million in rent and facilities expenses, $23.8 million in stock-based compensation expense (inclusive of employer payroll taxes), $19.8 million in acquired in-process research and development expense, $15.8 million in laboratory supplies, $8.4 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), $6.3 million in depreciation and amortization, $4.5 million in temporary labor, and contractors and $1.5 million in other operating expenses. These decreases were partially offset by an increase of $11.0 million in information technology expenses primarily due to a shortfall in contractually committed spending related to the our strategic cloud and AI partnership with Google Cloud (see Note 10 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q). General and Administrative Expenses General and administrative expenses were $45.0 million for the three months ended September 30, 2025, compared to $52.3 million for the three months ended September 30, 2024, a decrease of $7.3 million. This decrease was primarily driven by reductions of $6.4 million in personnel-related compensation and benefits expenses, $1.9 million in allocated overhead expenses (reclassified from R&D to G&A), $1.2 million of stock-based compensation expense (inclusive of employer payroll taxes), $1.4 million in earnout remeasurement expenses, $1.4 million in professional fees, and $0.7 million in other operating expenses. These decreases were partially offset by an increase of $5.7 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied. General and administrative expenses were $137.3 million for the nine months ended September 30, 2025, compared to $188.9 million for the nine months ended September 30, 2024, a decrease of $51.6 million. This decrease was primarily driven by reductions of $21.4 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $19.7 million in professional fees, $15.6 million in stock-based compensation expense (inclusive of employer payroll taxes), $7.9 million in earnout remeasurement expenses, $5.7 million in allocated overhead expenses (reclassified from R&D to G&A), $4.4 million in temporary labor and contractors, and $5.9 million in other operating expenses. These decreases were partially offset by an increase of $29.0 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied. Goodwill Impairment During the nine months ended September 30, 2024, we recorded a full impairment of the $47.9 million goodwill balance related to our Cell Engineering reporting unit. Restructuring Charges Restructuring charges were $1.7 million and $2.9 million for the three months ended September 30, 2025 and 2024, respectively, and $10.7 million and $20.0 million for the nine months ended September 30, 2025 and 2024, respectively. Restructuring charges relate to our restructuring plan, which was announced and commenced in the second quarter of 2024, primarily affecting the Cell Engineering segment. These charges primarily consisted of employee termination costs from 40 Table of Contents the reduction in force. See Note 3 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for further details. Interest Income, Net Interest income, net was $5.7 million for the three months ended September 30, 2025, compared to $9.3 million for the three months ended September 30, 2024, a decrease of $3.5 million primarily due to lower average cash balances invested in money market funds and marketable debt securities. Interest income, net was $17.9 million for the nine months ended September 30, 2025, compared to $31.3 million for the nine months ended September 30, 2024, a decrease of $13.4 million primarily due to lower average cash balances invested in money market funds and marketable debt securities. Gain (Loss) on Investments Gain on investments was $3.7 million for the three months ended September 30, 2025. Loss on investments was $6.9 million for the three months ended September 30, 2024. Loss on investments was $0.2 million and $16.3 million for the nine months ended September 30, 2025 and 2024, respectively. The change was primarily driven by fluctuations in the stock prices of marketable equity securities, partially offset by lower impairment losses on our non-marketable equity investments in privately held companies, compared to the same periods in 2024. We assess our non-marketable equity investments quarterly for potential impairment and remeasure them to fair value when events or changes in circumstances indicate that their carrying value may not be recoverable. Loss on Deconsolidation of Subsidiary In the third quarter of 2024, we recorded a $7.0 million loss on our deconsolidation of our former foreign subsidiary Altar as a result of a sale. Change in Fair Value of Warrant Liabilities The change in fair value of warrant liabilities was zero for both the three and nine months ended September 30, 2025, compared to gains of $1.5 million and $5.7 million for the three and nine months ended September 30, 2024, respectively. The fair value of warrant liabilities is primarily driven by fluctuations in the value of our common stock. An increase or decrease in the value of our common stock results in a loss or gain, respectively, in the fair value of warrant liabilities. As of September 30, 2025, these warrant liabilities had substantially no value. Other Income (Expense), Net We recorded a net other expense amount of $0.2 million for the three months ended September 30, 2025, compared to a net other income amount of $1.6 million for the three months ended September 30, 2024, a decrease of $1.7 million. We recorded a net other expense amount of $5.3 million for the nine months ended September 30, 2025, compared to a net other income amount of $2.8 million for the nine months ended September 30, 2024, a decrease of $8.2 million. This decrease was primarily due to losses on the change in fair value of a note receivable accounted for under the fair value option recorded in 2025. Non-GAAP Information In addition to our results determined in accordance with GAAP, we use earnings before interest, taxes, depreciation and amortization (“EBITDA”) and Adjusted EBITDA internally to evaluate our performance and make financial and operational decisions. We believe these non-GAAP measures, when viewed with our GAAP results, may be helpful to investors in assessing our operating performance. We define EBITDA as net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders before the impact of interest income, interest expense, provision for income taxes and depreciation and amortization. We define Adjusted EBITDA as EBITDA adjusted for stock-based compensation expense, gain or loss on equity method investments, gain or loss on investments, change in fair value of warrant liabilities, gain or loss on deconsolidation of subsidiaries, transaction and integration costs associated with planned, completed or terminated mergers and acquisitions, including related litigation costs, restructuring and impairment charges (inclusive of impairments of goodwill and long-lived assets), costs associated with the Zymergen Bankruptcy, and certain other income and expenses. We believe that the use of EBITDA and Adjusted EBITDA provides an additional tool for investors to use in evaluating ongoing operating 41 Table of Contents results and trends because it eliminates the effect of financing activities, investing activities, and certain non-cash charges and other items that are not related to our core operating performance or affect comparability period over period. Our non-GAAP financial measures have limitations as analytical tools and should not be considered in isolation or as a substitute for GAAP performance measures. These measures exclude significant expenses and income required by GAAP, which impacts their alignment with consolidated financial statements. They also rely on management’s judgment to determine which items are included or excluded, making them inherently subjective. Additionally, non-GAAP measures lack uniform definitions and may differ from those used by other companies, limiting comparability. A reconciliation of EBITDA and Adjusted EBITDA to net loss, the most directly comparable GAAP financial measure, is presented below: Three Months Ended September 30, Nine Months Ended September 30, (in thousands) 2025 2024 2025 2024 Net loss (1) $ (80,755) $ (56,403) $ (232,012) $ (439,495) Interest income, net (5,742) (9,251) (17,906) (31,275) Income tax (benefit) expense 1 (375) (194) (154) Depreciation and amortization 14,168 17,171 45,327 47,368 EBITDA (72,328) (48,858) (204,785) (423,556) Stock-based compensation (2) 18,103 14,013 61,429 94,636 Goodwill impairment — — — 47,858 Restructuring charges (3) 1,745 2,949 10,692 20,015 Merger and acquisition related expense (income) (4) 57 (796) (4,478) 6,110 Loss (gain) on investments (3,684) 6,912 238 16,282 Loss on deconsolidation of subsidiary — 7,013 — 7,013 Change in fair value of warrant liabilities — (1,528) — (5,701) Change in fair value of convertible notes 400 281 5,685 1,127 Adjusted EBITDA $ (55,707) $ (20,014) $ (131,219) $ (236,216) (1) All periods include non-cash revenue when earned, including $7.5 million recognized in the nine months ended September 30, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement. (2) Includes $0.3 million and $0.2 million in employer payroll taxes for the three months ended September 30, 2025 and 2024, respectively, and $0.9 million and $2.9 million for the nine months ended September 30, 2025 and 2024, respectively. (3) Restructuring charges primarily consist of employee termination costs from the reduction in force commenced in June 2024. (4) Represents transaction and integration costs directly related to mergers 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. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 2025 and 2024, respectively. Liquidity and Capital Resources On August 19, 2024, with the approval of our board of directors and shareholders, we effected a one-for-forty (1:40) reverse stock split for our common stock. Accordingly, all common shares presented herein relating to periods prior to this date have been retrospectively adjusted to reflect the reverse stock split. Sources of Liquidity Upon the closing of our merger with SRNG in September 2021, we received net proceeds totaling approximately $1.5 billion, inclusive of $760.0 million from investments from certain accredited investors for 1.9 million shares of our Class A 42 Table of Contents common stock. As of September 30, 2025, we had cash and cash equivalents and marketable securities of $461.9 million, which we believe will be sufficient to enable us to fund our projected operations through at least the next 12 months from the date of filing of this Quarterly Report on Form 10-Q. At-The-Market Program On August 7, 2025, we filed a universal shelf registration statement on Form S-3, which was declared effective by the SEC on August 14, 2024, on which we registered for sale up to $500 million of any combination of our Class A common stock, preferred stock, warrants, and/or units from time to time and at prices and on terms that we may determine. On September 4, 2025, the Company entered into 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 (the “Shares”) through or directly to the Agent in one or more at-the-market (“ATM”) offerings. Since inception of the Sales Agreement through September 30, 2025, the Company has issued 975,300 shares of Class A common stock under the ATM Sales Agreement for net proceeds of $9.4 million. We currently intend to use the net proceeds from this offering for general corporate purposes, which may include, but are not limited to, financing our operations, technology development, working capital and capital expenditures. Material Cash Requirements We anticipate that our expenditures will exceed our revenue through at least the next 12 months from the date of filing of this Quarterly Report on Form 10-Q, as we: • continue our R&D activities under existing and new programs and further invest in our Foundry and Codebase; • develop and expand our tools offerings; • upgrade or adapt our operational, financial and management systems and support our operations; • potentially acquire and integrate companies, assets or intellectual property that advance our company objectives; • maintain, expand, and protect our intellectual property; and • continue our restructuring actions. Cash Flows The following table provides information regarding our cash flows for each period presented: Nine Months Ended September 30, (in thousands) 2025 2024 Net cash provided by (used in): Operating activities $ (123,381) $ (277,150) Investing activities (335,388) (49,151) Financing activities 9,633 (1,536) Effect of exchange rate changes 353 (208) Net decrease in cash, cash equivalents and restricted cash $ (448,783) $ (328,045) Operating Activities Net cash used in operating activities for the nine months ended September 30, 2025 consisted of a net loss of $232.0 million, adjusted for net change in operating assets and liabilities of $20.5 million and non-cash charges of $129.1 million. The net change in operating assets and liabilities was primarily due to (i) a $27.2 million decrease in deferred revenue primarily from one-time releases of deferred revenue balances associated with terminated customer contracts and the recognition of previously deferred revenue, (ii) a $18.8 million decrease in operating lease liabilities from rent payments, and (iii) a $0.3 million increase in accounts receivable due to timing of customer billings, partially offset by (iv) a $17.0 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation, and (v) a $3.8 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $60.5 million of stock-based compensation expense, 43 Table of Contents $45.3 million of depreciation and amortization, $22.4 million non-cash lease expense, a $1.5 million change in fair values of various assets and liabilities, $2.5 million accretion of discount on marketable securities, and a $0.3 million loss on investments. Net cash used in operating activities for the nine months ended September 30, 2024 consisted of a net loss of $439.5 million, adjusted for a net decrease in cash due to changes in operating assets and liabilities of $91.8 million and non-cash charges of $254.2 million. The net change in operating assets and liabilities was primarily driven by a $31.1 million decrease in accounts payable, accrued expenses and other current liabilities primarily due to the payment or release of restructuring-related accruals and litigation costs, a $67.8 million decrease in deferred revenue primarily from a one-time release of a deferred revenue balance associated with a terminated customer contract, and a $11.4 million decrease in operating lease liabilities from rent payments, partially offset by a $19.2 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $47.4 million in depreciation and amortization, $91.8 million in stock-based compensation expense, $16.3 million loss on investments, $20.6 million non-cash lease expense, $19.8 million in acquired in-process research and development expense, and $47.9 million in goodwill impairment. Investing Activities Net cash used in investing activities for the nine months ended September 30, 2025 primarily consisted of purchases of marketable debt securities of $401.8 million, maturities of marketable debt securities of $73.6 million, and purchases of property and equipment of $7.7 million related to the build-out of new office and laboratory space near our headquarters. Net cash used in investing activities for the nine months ended September 30, 2024 primarily consisted of $48.8 million in purchases of property and equipment related to Foundry capacity and capability investments, $5.4 million paid for the acquisition of certain Zymergen assets, and $4.0 million in proceeds from the sale of investment securities. Financing Activities Net cash provided by financing activities for the nine months ended September 30, 2025 primarily consisted of $10.0 million in net proceeds from an ATM offering and $0.3 million of principal payments on finance leases. Net cash used in financing activities for the nine months ended September 30, 2024 primarily consisted of $0.7 million of principal payments on finance leases and $0.9 million in payments of contingent consideration related to business acquisitions. Critical Accounting Estimates There have been no material changes to our critical accounting estimates as compared to the critical accounting estimates disclosed in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our 2024 Annual Report. Recently Issued Accounting Pronouncements See Note 1 , “Basis of Presentation and Summary of Significant Accounting Policies,” of our condensed consolidated financial statements contained in Part I, Item 1 of this Quarterly Report on Form 10-Q for a discussion of recently issued accounting pronouncements, as disclosed in our 2024 Annual Report.