UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.     )*

Ginkgo Bioworks Holdings, Inc.

(Name of Issuer)

Class A Common Stock

(Title of Class of Securities)

37611X100

(CUSIP Number)

c/o Ginkgo Bioworks Holdings, Inc.

27 Drydock Avenue, 8^th Floor

Boston, MA 02210

(877) 422-5362

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

September 16, 2021

(Date of Event Which Requires Filing of This Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), Rule 13d-1(f) or Rule 13d-1(g), check the following box.   ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7(b) for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

This statement on Schedule 13D (the “Schedule 13D”) relates to the shares of Class A Common Stock, par value $0.0001 per share (the “Class A Common Stock”), of Ginkgo Bioworks Holdings, Inc., a Delaware corporation (the “Issuer”), whose principal executive office is located at 27 Drydock Avenue, 8th Floor, Boston, MA 02210. Prior to the Business Combination (as defined below), the Issuer was known as Soaring Eagle Acquisition Corp. (“SRNG”).

The Schedule 13D is being filed by Jason Kelly (the “Reporting Person”), a citizen of the United States. The business address of the Reporting Person is c/o Ginkgo Bioworks Holdings, Inc., 27 Drydock Avenue, 8th Floor, Boston, MA 02210. The Reporting Person’s present principal occupation is Chief Executive Officer, Founder and Director of the Issuer.

During the last five years, the Reporting Person has not been (i) convicted in any criminal proceeding (excluding traffic violations or similar misdemeanors) or (ii) a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Item 4 below summarizes certain provisions of the Merger Agreement (as defined below) that pertain to the securities acquired by the Reporting Person. Pursuant to the Merger Agreement, upon consummation of the Business Combination (as defined below), the Reporting Person received 82,581,106 shares of Class B common stock, par value $0.0001 per share, of the Issuer (the “Class B Common Stock”) that may be redeemed by the Reporting Person at any time for shares of Class A Common Stock on a one-to-one basis.

Business Combination

On September 16, 2021 (the “Closing Date”), pursuant to an agreement and plan of merger, dated as of May 11, 2021, as amended on May 14, 2021 (the “Merger Agreement”), by and among SRNG, SEAC Merger Sub Inc., a Delaware corporation and wholly owned subsidiary of SRNG (the “Merger Sub”) and Ginkgo Bioworks, Inc. (“Old Ginkgo”), Merger Sub merged with and into Old Ginkgo with Old Ginkgo being the surviving company in the merger (the “Merger” and, together with the other transactions contemplated by the Merger Agreement, the “Business Combination”). As a result of the Merger, the Issuer directly owns 100% of the outstanding common stock of Old Ginkgo as the surviving company in the Merger and each share of common stock of Old Ginkgo outstanding immediately prior to the effective time of the Business Combination was cancelled and extinguished and collectively converted into the right to receive shares of Class A Common Stock and/or Class B Common

Stock, in accordance with the Merger Agreement, on a 1-to-49.080452 basis. In addition, each share of common stock of Old Ginkgo, each option of Old Ginkgo under Old Ginkgo’s stock incentive plans, each award of restricted common stock of Old Ginkgo under Old Ginkgo’s stock incentive plans, and each award of restricted stock units of Old Ginkgo under Old Ginkgo’s stock incentive plans, in each case outstanding immediately prior to the effective time of the Business Combination, received a proportional amount of the approximately 188.7 million earn-out shares. As a result of the Business Combination, the Reporting Person received 70,971,021 shares of Class B Common Stock and an additional 11,610,085 shares of the Class B Common Stock in the form of earn-out shares subject to forfeiture, which will vest in four substantially equal installments if the Class A Common Stock achieves a price per share for any period of 20 trading days out of 30 consecutive trading days prior to September 16, 2026 that equals or exceeds the following thresholds: $12.50, $15.00, $17.50 and $20.00.

Lock-Up

On the Closing Date, in connection with the closing of the Business Combination, the Issuer adopted a certificate of incorporation with a lock-up provision applicable to the Reporting Person. The provision provides that such individuals are restricted from transferring their shares of Class A Common Stock or Class B Common Stock received as consideration in the Business Combination, excluding the earn-out shares, for a period of one year following the closing of the Business Combination (the “Transfer Restrictions”). The Transfer Restrictions will not apply to an aggregate of 10% of the total number of shares subject to such restrictions, excluding (from this exception to the Transfer Restrictions) any shares of Class A Common Stock or Class B Common Stock received upon the settlement of an equity award that was converted in the Merger. Additionally, solely in the case of a holder of any equity award of the Issuer (including any such equity award into which an equity award of Old Ginkgo was converted in the Merger), the Transfer Restrictions will be lifted beginning on the earlier of March 1, 2022 or the date that is 15 calendar days before the date on which any tax relating to such equity award (other than any equity or portion thereof that is exempted from such Transfer Restrictions) will become due under applicable law, subject to certain conditions.

General

The Reporting Person acquired the securities described in this Schedule 13D in connection with the closing of the Business Combination and intends to review his investments in the Issuer on a continuing basis. Any actions the Reporting Person might undertake may be made at any time and from time to time without prior notice and will be dependent upon the Reporting Person’s review of numerous factors, including, but not limited to: an ongoing evaluation of the Issuer’s business, financial condition, operations and prospects; price levels of the Issuer’s securities; general market, industry and economic conditions; the relative attractiveness of alternative business and investment opportunities; and other future developments.

The Reporting Person may acquire additional securities of the Issuer, or retain or sell all or a portion of the securities then held, in the open market or in privately negotiated transactions. In addition, the Reporting Person may engage in discussions with management, the Issuer’s board of directors, and other securityholders of the Issuer and other relevant parties or encourage,

cause or seek to cause the Issuer or such persons to consider or explore extraordinary corporate transactions, such as: a merger, reorganization or take-private transaction that could result in the de-listing or de-registration of the Class A Common Stock; sales or acquisitions of assets or businesses; changes to the capitalization or dividend policy of the Issuer; or other material changes to the Issuer’s business or corporate structure, including changes in management or the composition of the board of directors.

Other than as described above, the Reporting Person does not currently have any plans or proposals that relate to, or would result in, any of the matters listed in Items 4(a)–(j) of Schedule 13D, although, depending on the factors discussed herein, the Reporting Person may change his purpose or formulate different plans or proposals with respect thereto at any time.

(a) – (b)

The share amount reported herein consists of (i) 70,853,049 shares of Class B Common Stock held of record by the Reporting Person and (ii) 11,728,057 shares of Class B Common Stock held of record by the Reporting Person’s grantor retained annuity trust, over which the Reporting Person serves as trustee.

The above percentage is based on 1,330,072,374 shares of Class A Common Stock outstanding following completion of the Business Combination.

The Reporting Person does not have any contracts, arrangements, understandings or relationships (legal or otherwise) with any person with respect to any securities of the Issuer, including but not limited to any contracts, arrangements, understandings or relationships concerning the transfer or voting of such securities, finder’s fees, joint ventures, loan or option arrangements, puts or calls, guarantees of profits, division of profits or losses, or the giving or withholding of proxies.

None.

SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date: September 27, 2021