UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)*

Morphic Holding, Inc.

(Name of Issuer)

Common Stock, par value $0.0001 per share

(Title of Class of Securities)

61775R105

(CUSIP Number)

Barbara Fiorini Due

Novo Holdings A/S

Tuborg Havnevej 19

Hellerup, Denmark DK-2900

+45 3527 6592

Copy to:

B. Shayne Kennedy, Esq.

Latham & Watkins LLP

650 Town Center Drive, 20^th Floor

Costa Mesa, CA 92626

Telephone: (714) 540-1235

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

November 1, 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 which is subject of this Schedule 13D, and is filing this statement because of Rule 13d-1(e), 13d-1(f) or 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 (the “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).

CUSIP No.: 61775R105

2

This Amendment No. 3 amends Schedule 13D originally filed with the SEC on July 1, 2019, as subsequently amended by Amendment No. 1 filed on March 11, 2021 and Amendment No. 2 filed on August 12, 2021 (collectively, the “Schedule”) to report and reflect that effective November 1, 2021 Nilesh Kumar, Ph.D., a board member of the Issuer, ceased employment with Novo Ventures (US), Inc. and thus is no longer affiliated with Novo Holdings A/S.

Except as specifically amended by this Amendment No. 3, each Item of the Schedule remains unchanged. All capitalized terms contained herein but not otherwise defined shall have the meanings ascribed to such terms in the Schedule

Item 2 (a) of the Schedule is amended and replaced in its entirety as follows:

The name of each director and executive officer of both Novo Holdings A/S and the Foundation is set forth on Schedule I to this Schedule 13D.

Item 4 of the Schedule is amended and replaced in its entirety as follows:

The acquisitions of Issuer securities made by Novo Holdings A/S, as described in this Schedule 13D, were for investment purposes. Novo Holdings A/S intends to review its investments in the Issuer on a continuing basis and any actions Novo Holdings A/S might undertake will be dependent upon its review of numerous factors from time to time, 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. Novo Holdings A/S may, at any time and from time to time, acquire additional securities of the Issuer, or retain or sell all or a portion of the securities of the Issuer then held, in the open market or in privately negotiated transactions.

Nilesh Kumar, Ph.D. was appointed to the board of directors of the Issuer in July 2017. Effective as of November 1, 2021, Dr. Kumar is no longer employed by Novo Ventures (US), Inc., and is no longer affiliated with Novo Holdings A/S. Dr. Kumar is not, and has not been, deemed to be a beneficial owner of the securities held by Novo Holdings A/S. Other than as described herein, Novo Holdings A/S currently does not 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, Novo Holdings A/S may review or reconsider or change its purpose or formulate different plans, strategies, or proposals with respect thereto at any time.

Item 5 of the Schedule is amended and replaced in its entirety as follows:

3

(a) Novo Holdings A/S beneficially owns 2,050,446 shares of Common Stock (the “Novo Shares”) representing approximately 5.6% of the Issuer’s outstanding shares of Common Stock, Based upon 36,451,080 shares of the Issuer’s Common Stock outstanding as of August 2, 2021, as reported in the Issuer’s Form S-3 Registration Statement filed with the SEC on August 4, 2021.

(b) Novo Holdings A/S is a Danish corporation wholly owned by the Novo Nordisk Foundation. Novo Holdings A/S has the sole power to vote and dispose of the Novo Shares. Neither the Foundation nor any person listed on Schedule I is deemed to have any beneficial ownership in the Novo Shares.

(c) On August 6, 2021, Novo Holdings A/S sold 595,000 shares of the Issuer’s Common Stock at a price per shares of $53.75 (which sale was inadvertently not included in Item 5(c) of Amendment 2 to Schedule 13D filed on August 12, 2021), and except for this sale Novo Holdings has not effected any transactions in the Issuer’s Common Stock within the past 60 days. The Foundation nor any person listed on Schedule I has effected any transactions in the Issuer’s Common Stock within the past 60 days.

(d) Novo Holdings A/S does not know of any other person having the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of the Novo Shares.

(e) Not applicable.

4

SIGNATURE

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.

Schedule I

Information regarding each director and executive officer of both Novo Holdings A/S and the Novo Nordisk Foundation is set forth below.