Ginkgo Bioworks Holdings Inc

To the stockholders and the Board of Directors of Ginkgo Bioworks Holdings, Inc.

Opinion on the Financial Statements

We have audited the accompanying consolidated balance sheet of Ginkgo Bioworks Holdings, Inc. and subsidiaries (the “Company”) as of December 31, 2024, and the related consolidated statements of operations and comprehensive loss, stockholders' equity, and cash flows for the year ended December 31, 2024, and the related notes (collectively referred to as the “financial statements”). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Company as of December 31, 2024, and the results of its operations and its cash flows for the year ended December 31, 2024, in conformity with accounting principles generally accepted in the United States of America.

We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the Company’s internal control over financial reporting as of December 31, 2024, based on criteria established in Internal Control — Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission and our report dated February 25, 2025, expressed an unqualified opinion on the Company’s internal control over financial reporting.

These financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on the Company’s financial statements based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. Our audit included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audit also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audit provides a reasonable basis for our opinion.

Critical Audit Matters

The critical audit matters communicated below are matters arising from the current-period audit of the financial statements that were communicated or required to be communicated to the audit committee and that (1) relate to accounts or disclosures that are material to the financial statements and (2) involved our especially challenging, subjective, or complex judgments. The communication of critical audit matters does not alter in any way our opinion on the financial statements, taken as a whole, and we are not, by communicating the critical audit matters below, providing separate opinions on the critical audit matters or on the accounts or disclosures to which they relate.

Cell Engineering Revenue Recognition — Refer to Notes 2 and 14 to the financial statements

Critical Audit Matter Description

The Company generates Cell Engineering revenue primarily through license and collaboration agreements, under which customers obtain rights to the Company’s proprietary technology and intellectual property for use in the research, development and commercialization of engineered organisms and derived products. Under these agreements, the Company typically provides research and development services, including granting a license to its intellectual property. Additionally, the customer may obtain license rights to the output of the Company’s services in order to commercialize the resulting output of such services. Cell Engineering revenue was $174 million for the year ended December 31, 2024.

The Company generally recognizes Cell Engineering revenue over time based on the cost incurred to date relative to total expected costs or for cost-plus contracts, as costs are incurred. The Company evaluates its measure of progress to recognize revenue at each reporting period and, as necessary, adjusts the measure of progress and related revenue recognition. The Company’s measure of progress and revenue recognition involves significant judgment and assumptions, including, but not limited to, evaluating contract terms and estimating the cost to complete the performance obligation.

Auditing the Cell Engineering revenue was challenging due to the extent of audit effort required to evaluate the volume and complexity of customer contracts, including estimates of the measure of progress.

How the Critical Audit Matter Was Addressed in the Audit

Our audit procedures related to Cell Engineering revenue included the following, among others:

•We selected a sample of Cell Engineering contracts and performed the following:

◦Evaluated whether the contracts were properly included in management’s calculation of Cell Engineering revenue based on the terms and conditions of each contract, including whether continuous transfer of control to the customer occurred as progress was made toward fulfilling the performance obligation(s).

◦Compared the transaction price to the consideration expected to be received based on current rights and obligations under the contracts and any modifications that were agreed upon with the customers.

◦Tested management’s identification of distinct performance obligations.

◦To the extent a contract did not represent a single distinct performance obligation, we tested the allocation of the transaction price to each distinct performance obligation by comparing the relative standalone selling prices to the selling prices of similar goods or services.

◦Tested the accuracy and completeness of the costs incurred to date for each performance obligation.

◦Evaluated the estimates of total cost incurred and total estimated cost, when applicable, for the performance obligation by:

▪Testing the costs incurred to date.

▪Evaluating management’s estimates of total cost by performing corroborating inquiries with those that are responsible for managing the contract execution, and comparing the estimates to management’s work plans.

◦Tested the mathematical accuracy of management’s calculation of revenue for the performance obligation.

•We evaluated management’s ability to estimate total costs accurately by comparing actual costs to management’s historical estimates for performance obligations that have been fulfilled.

Goodwill Impairment — Refer to Notes 2 and 8 to the financial statements

Critical Audit Matter Description

The Company’s assessment of goodwill for impairment involves the comparison of the fair value of the reporting unit to its carrying value. The Company used a discounted cash flow model and guideline public company method to estimate fair value of its Cell Engineering reporting unit, which requires management to make significant estimates and assumptions related to projected future operating results, discount rates, and peer company multiples. Changes in these assumptions could have a significant impact on either the fair value of the Cell Engineering reporting unit, the amount of any goodwill impairment charge, or both.

As a result of an indicator of impairment, the Company performed an interim goodwill impairment assessment as of June 30, 2024, and determined that the fair value of the Cell Engineering reporting unit was less than its carrying value and that the goodwill was fully impaired. As a result, a goodwill impairment charge of $47.9 million was recorded in the year ended December 31, 2024.

Given the Company’s determination of the fair value of its Cell Engineering reporting unit required management to make significant estimates and assumptions related to projected future operating results, discount rates, and peer company multiples, auditing the reasonableness of the assumptions used involved especially subjective judgment and an increased extent of effort, including the need to involve of our fair value specialists. We identified goodwill as a critical audit matter because of the significant judgments made by management to estimate the fair value of the Cell Engineering reporting unit.

How the Critical Audit Matter Was Addressed in the Audit

Our audit procedures related to the projected future operating results, discount rates, and peer company multiples used by management to estimate the fair value of the Cell Engineering reporting unit included the following, among others:

•We evaluated the reasonableness of management’s projected future operating results by comparing the projections to (1) historical operating results, (2) internal communications to management and the Board of Directors, (3) information included in analyst and industry reports as well as certain publicly available peer company information, and (4) comparing actual results to management’s historical forecasts.

•With the assistance of our fair value specialists, we evaluated the reasonableness of the valuation methodology, discount rates and peer company multiples by:

◦Testing the source information underlying the determination of the discount rates and peer company multiples, and the mathematical accuracy of the calculations.

◦Developing a range of independent estimates and comparing those to the discount rates and peer company multiples selected by management.

/s/Deloitte & Touche LLP

February 25, 2025

We have served as the Company’s auditor since 2024.

To the Stockholders and the Board of Directors of Ginkgo Bioworks Holdings, Inc.

Opinion on the Financial Statements

We have audited the accompanying consolidated balance sheet of Ginkgo Bioworks Holdings, Inc. (the Company) as of December 31, 2023, the related consolidated statements of operations and comprehensive loss, stockholders’ equity and cash flows for each of the two years in the period ended December 31, 2023, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2023, and the results of its operations and its cash flows for each of the two years in the period ended December 31, 2023, in conformity with U.S. generally accepted accounting principles.

These financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company’s financial statements based on our audits. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

/s/ Ernst & Young LLP

We served as the Company’s auditor from 2018 to 2024.

February 29, 2024, except for note 15 and the effects of the reverse stock split described in note 2, as to which the date is February 25, 2025