UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 13D

(Rule 13d-101)

Information to be Included in Statements Filed Pursuant

to § 240.13d-1(a) and Amendments Thereto Filed

Pursuant to § 240.13d-2(a)

Under the Securities Exchange Act of 1934

(Amendment No. 3)

NewAmsterdam Pharma Company N.V.

(Name of Issuer)

Ordinary Shares, nominal value €0.12 per share

(Title of Class of Securities)

N62509109

(CUSIP Number)

Bain Capital Life Sciences Investors, LLC

200 Clarendon Street

Boston, MA 02116

617-516-2000

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

December 13, 2024

(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 §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-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 § 240.13d-7 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, as amended (“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).

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering (as defined herein); and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering; and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering; and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering; and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering; and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering; and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

This Amendment No. 3 to Schedule 13D relates to the Ordinary Shares, nominal value €0.12 per share (the “Ordinary Shares”), of NewAmsterdam Pharma Company N.V., a public limited liability company incorporated in the Netherlands (the “Issuer”), and amends the initial statement on Schedule 13D filed by the Reporting Persons on December 2, 2022, as amended by Amendment No. 1 filed on June 13, 2023 and Amendment No. 2 filed on March 1, 2024 (the “Initial Statement” and, as further amended by this Amendment No. 3, the “Schedule 13D”). Capitalized terms used but not defined herein shall have the meanings ascribed to them in the Initial Statement.

Item 2 of the Initial Statement is hereby amended and restated as follows:

(a) This Schedule 13D is being filed jointly by BCLS Fund III Investments, LP, a Delaware limited partnership (“BCLS Fund III”), Bain Capital Life Sciences Opportunities III, LP, a Delaware limited partnership (“BCLS Fund III Opportunities”), Bain Capital Life Sciences Fund II, L.P., a Cayman Islands exempted limited partnership (“BCLS Fund II”), BCLS II Investco, LP, a Delaware limited partnership (“BCLS II Investco”), BCLS II Equity Opportunities, LP, a Delaware limited partnership (“BCLS Fund II Opportunities”), and BCIP Life Sciences Associates, LP, a Delaware limited partnership (“BCIPLS” and, together with BCLS Fund III, BCLS Fund III Opportunities, BCLS Fund II, BCLS II Investco and BCLS Fund II Opportunities, the “Reporting Persons”).

Bain Capital Life Sciences Investors, LLC, a Delaware limited liability company (“BCLSI”), is the manager of Bain Capital Life Sciences III General Partner, LLC, a Delaware limited liability company (“BCLS III GP”), which is the general partner of Bain Capital Life Sciences Fund III, L.P., a Delaware limited partnership (“BCLS III”), which is the managing member of BCLS Fund III Investments GP, LLC, a Delaware limited liability company (“BCLS Fund III GP”), which is the general partner of BCLS Fund III. BCLS III is also the sole member of Bain Capital Life Sciences Opportunities III GP, LLC, a Delaware limited liability company (“BCLS Fund III Opportunities GP”), which is the general partner of BCLS Fund III Opportunities.

BCLSI is also the manager of Bain Capital Life Sciences Investors II, LLC, a Cayman Islands limited liability company (“BCLSI II”), which is the general partner of BCLS Fund II, which is the managing member of BCLS II Investco (GP), LLC, a Delaware limited liability company (“BCLS II Investco GP”), which is the general partner of BCLS II Investco. BCLS Fund II is also the manager of BCLS II Equity Opportunities GP, LLC, a Delaware limited liability company (“BCLS Fund II Opportunities GP”), which is the general partner of BCLS Fund II Opportunities.

Boylston Coinvestors, LLC, a Delaware limited liability company (“Boylston” and, together with the Reporting Persons, BCLSI, BCLS III GP, BCLS III, BCLS Fund III GP, BCLS Fund III Opportunities GP, BCLSI II, BCLS II Investco GP and BCLS Fund II Opportunities GP, the “Bain Capital Life Sciences Entities”), is the general partner of BCIPLS. BCLSI governs the investment strategy and decision-making process with respect to investments held by BCIPLS.

As a result, BCLSI may be deemed to share voting and dispositive power with respect to the securities held by the Reporting Persons.

The Reporting Persons have entered into a Joint Filing Agreement, dated December 17, 2024, pursuant to which the Reporting Persons have agreed to file this Schedule 13D jointly in accordance with the provisions of Rule 13d-1(k)(1) promulgated under the Act.

(b) The principal business address for each of the Bain Capital Life Sciences Entities is 200 Clarendon Street, Boston, Massachusetts 02116.

(c) Each of the Bain Capital Life Sciences Entities is principally engaged in the business of investment in securities.

(d) During the last five years, none of the Bain Capital Life Sciences Entities have been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

(e) During the last five years, none of the Bain Capital Life Sciences Entities have been 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 violation of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

(f) BCLS Fund II and BCLSI II are organized under the laws of the Cayman Islands. BCLS Fund III, BCLS Fund III Opportunities, BCLS II Investco, BCLS Fund II Opportunities, BCIPLS, BCLSI, BCLS III GP, BCLS III, BCLS Fund III GP, BCLS Fund III Opportunities GP, BCLS II Investco GP, BCLS Fund II Opportunities GP and Boylston are organized under the laws of the State of Delaware.

Item 3 of the Initial Statement is hereby amended and supplemented to add the following:

On December 11, 2024 the Issuer entered into an underwriting agreement with Jefferies LLC, Goldman Sachs & Co. LLC, Leerink Partners LLC, TD Securities (USA) LLC, Guggenheim Securities, LLC and William Blair & Company, L.L.C., as representatives of the several underwriters, related to a public offering (the “December 2024 Offering”) of 14,667,347 Ordinary Shares (inclusive of the full exercise of the underwriters’ option to purchase additional shares) and, in lieu of Ordinary Shares to certain investors, Pre-Funded Warrants (the “Pre-Funded Warrants”) to purchase an aggregate of 4,882,653 Ordinary Shares. The Ordinary Shares were sold at a public offering price of $24.50 per share and the Pre-Funded Warrants were sold at a public offering price of $24.4999 per Ordinary Share underlying each Pre-Funded Warrant. The December 2024 Offering closed on December 13, 2024.

In the December 2024 Offering, BCLS Fund III Opportunities purchased a Pre-Funded Warrant to purchase 1,257,141 Ordinary Shares for a purchase price of $30,799,828.79 and BCLS Fund II Opportunities purchased a Pre-Funded Warrant to purchase 375,512 Ordinary Shares for a purchase price of $9,200,006.45. BCLS Fund III Opportunities and BCLS Fund II Opportunities each used their own working capital to acquire the securities.

Item 5 of the Initial Statement is hereby amended and restated as follows:

The information set forth in Items 2, 3 and 6 and on the cover pages of this Schedule 13D is incorporated by reference in its entirety into this Item 5.

(a) – (c) As of the date hereof, (i) BCLS Fund III directly holds 5,376,356 Ordinary Shares; (ii) BCLS Fund III Opportunities directly holds a Pre-Funded Warrant to purchase 1,257,141 Ordinary Shares; (iii) BCLS Fund II directly holds 267,429 Ordinary Shares and a Warrant to purchase 89,143 Ordinary Shares; (iv) BCLS II Investco directly holds 4,797,557 Ordinary Shares; (v) BCLS Fund II Opportunities directly holds a Pre-Funded Warrant to purchase 375,512 Ordinary Shares; and (vi) BCIPLS directly holds 32,571 Ordinary Shares and a Warrant to purchase 10,857 Ordinary Shares.

As a result of the Beneficial Ownership Blocker (as defined below), BCLS Fund III Opportunities and BCLS Fund II Opportunities are precluded from exercising Pre-Funded Warrants to the extent that the Reporting Persons would, after such exercise, collectively beneficially own in excess of 9.99% of the outstanding Ordinary Shares. Accordingly, pursuant to Rule 13d-3 of the Act and the relationships described in Item 2 of this Schedule 13D, the Reporting Persons may be deemed to collectively beneficially own 9.99% of the outstanding Ordinary Shares, representing 10,719,110 Ordinary Shares as of the date hereof.

The calculation of the beneficial ownership of the Reporting Persons is based on (i) 92,385,872 Ordinary Shares issued and outstanding as of October 31, 2024, as reported by the Issuer in its Quarterly Report on Form 10-Q for the quarter ended September 30, 2024; (ii) 14,667,347 Ordinary Shares issued in the December 2024 Offering; and (iii) 245,197 Ordinary Shares to be issued upon the exercise of the Warrants and Pre-Funded Warrants held by the Reporting Persons, which reflects the Beneficial Ownership Blocker.

(d) Except as otherwise described in this Item 5, no one other than the Reporting Persons has the right to receive, or the power to direct the receipt of, dividends from, or the proceeds from the sale of, any of the Ordinary Shares beneficially owned by the Reporting Persons as described in this Item 5.

(e) Not applicable.

Item 6 of the Initial Statement is hereby amended and supplemented to add the following:

December 2024 Lock-Up Agreement

In connection with the December 2024 Offering, BCLS Fund III, BCLS Fund II, BCLS II Investco, BCIPLS and Dr. Downing each entered into a lock-up agreement (the “December 2024 Lock-Up Agreement”) with the representatives of the several underwriters of the December 2024 Offering, pursuant to which they each agreed, subject to certain exceptions, not to sell or offer to sell any Ordinary Shares or securities convertible into or exercisable or exchangeable for, Ordinary Shares for a period of 45 days after the date of the prospectus relating to the December 2024 Offering without the prior written consent of each of Jefferies LLC and Goldman Sachs & Co. LLC.

The foregoing summary of the December 2024 Lock-Up Agreement does not purport to be complete and is qualified in its entirety by reference to the December 2024 Lock-Up Agreement, which is filed as an exhibit hereto and incorporated by reference herein.

Pre-Funded Warrant

Exercisability. Each Pre-Funded Warrant is exercisable at any time after its original issuance solely by means of a cashless exercise.

Exercise Blocker. The holder of a Pre-Funded Warrant is prohibited from exercising the Pre-Funded Warrant into Ordinary Shares if, as a result of such exercise, the holder, together with its affiliates and any other persons whose beneficial ownership would be aggregated with the holder’s for purposes of Section 13(d) of the Act, would beneficially own more than 9.99% of the total number of Ordinary Shares then issued and outstanding immediately after giving effect to the exercise (the “Beneficial Ownership Blocker”). Each of BCLS Fund III Opportunities and BCLS Fund II Opportunities has delivered written notice to the Issuer to irrevocably forfeit their right to increase the Beneficial Ownership Blocker above 9.99%.

Exercise Price. The exercise price per Ordinary Share purchasable upon the exercise of the Pre-Funded Warrant is $0.0001 per Ordinary Share. The exercise price is subject to appropriate adjustment in the event of certain stock dividends and distributions, stock splits, stock combinations, or reclassifications affecting the Ordinary Shares.

Transferability. Subject to compliance with applicable securities laws, each Pre-Funded Warrant may be transferred or assigned by the holder thereof without the Issuer’s consent.

Fundamental Transaction. If a Fundamental Transaction (as defined in the Pre-Funded Warrant) occurs while a Pre-Funded Warrant is outstanding, then upon any subsequent exercise of the Pre-Funded Warrant, the holder thereof has the right to receive the same amount and kind of securities, cash or property as such holder would have been entitled to receive upon the occurrence of such Fundamental Transaction if it had been, immediately prior to such Fundamental Transaction, the holder of the number of Ordinary Shares then issuable upon exercise in full of the Pre-Funded Warrant (without regard to any limitations on exercise).

Rights as a Stockholder. Except as otherwise provided in the Pre-Funded Warrant or by virtue of the holder’s ownership of Ordinary Shares, the holder of a Pre-Funded Warrant does not have the rights or privileges of a holder of Ordinary Shares, including any voting rights, until the holder exercises the Pre-Funded Warrant.

The foregoing summary of the Pre-Funded Warrant does not purport to be complete and is qualified in its entirety by reference to the form of Pre-Funded Warrant, which is filed as an exhibit hereto and incorporated by reference herein.

Item 7 of the Initial Statement is hereby amended and supplemented to add the following:

SIGNATURES

After reasonable inquiry and to the best of its knowledge and belief, the undersigned certifies that the information set forth in this statement is true, complete and correct.

Exhibit I

AGREEMENT REGARDING THE JOINT FILING OF

SCHEDULE 13D

The undersigned being duly authorized thereunto, hereby execute this agreement as an exhibit to this Schedule 13D to evidence the agreement of the below-named parties, in accordance with the rules promulgated pursuant to the Securities Exchange Act of 1934, as amended, to file this Schedule 13D (including amendments thereto) jointly on behalf of each such party.