X0202 SCHEDULE 13G 0001400240 XXXXXXXX LIVE Common Stock, $0.001 par value per share 03/31/2026 0002100782 Generate Biomedicines, Inc. 370920100 101 South Street, Suite 900 Somerville MA 02143 Rule 13d-1(d) Flagship Pioneering Fund VI, L.P. b DE 0 12723940 0 12723940 12723940 N 9.9 PN Flagship Pioneering Fund VI General Partner LLC b DE 0 12723940 0 12723940 12723940 N 9.9 OO Pioneering Medicines 02, LLC b DE 0 1562500 0 1562500 1562500 N 1.2 OO Flagship Pioneering Fund VII, L.P. b DE 0 16827224 0 16827224 16827224 N 13.1 PN Flagship Pioneering Fund VII General Partner LLC b DE 0 16827224 0 16827224 16827224 N 13.1 OO Nutritional Health LTP Fund, L.P. b DE 0 987491 0 987491 987491 N 0.8 PN Nutritional Health LTP Fund General Partner LLC b DE 0 987491 0 987491 987491 N 0.8 PN Flagship Pioneering Special Opportunities Fund II, L.P. b DE 0 2777752 0 2777752 2777752 N 2.2 PN Flagship Pioneering Special Opportunities Fund II General Partner LLC b DE 0 2777752 0 2777752 2777752 N 2.2 OO FPN II, L.P. b A6 0 4340252 0 4340252 4340252 N 3.4 PN FPN General Partner LLC b DE 0 4340252 0 4340252 4340252 N 3.4 OO Flagship VentureLabs VI, LLC b DE 0 25016458 0 25016458 25016458 N 19.5 OO Flagship VentureLabs VI Manager LLC b DE 0 25016458 0 25016458 25016458 N 19.5 OO Flagship Pioneering, LLC b DE 0 62673117 0 62673117 62673117 N 48.9 OO Afeyan Noubar b X1 28798 62673117 28798 62673117 62701915 N 48.9 IN Generate Biomedicines, Inc. 101 South Street, Suite 900, Somerville, MA 02143 The names of the persons filing this report (collectively, the "Reporting Persons") are: (i) Flagship Pioneering Fund VI, L.P. ("Flagship Fund VI"). (ii) Flagship Pioneering Fund VI General Partner LLC ("Flagship Fund VI GP"). (iii) Pioneering Medicines 02, LLC ("PM02"). (iv) Flagship Pioneering Fund VII, L.P. ("Flagship Fund VII"). (v) Flagship Pioneering Fund VII General Partner LLC ("Flagship Fund VII GP"). (vi) Nutritional Health LTP Fund, L.P. ("Nutritional LTP"). (vii) Nutritional Health LTP Fund General Partner LLC ("Nutritional LTP GP"). (viii) Flagship Pioneering Special Opportunities Fund II, L.P. ("Flagship Opportunities Fund II"). (ix) Flagship Pioneering Special Opportunities Fund II General Partner LLC ("Flagship Opportunities Fund II GP"). (x) FPN II, L.P. ("FPN II Fund"). (xi) FPN General Partner LLC ("FPN GP"). (xii) Flagship VentureLabs VI, LLC ("VentureLabs VI" and together with Flagship Fund VI, PM02, Flagship Fund VII, Nutritional LTP, Flagship Opportunities Fund II and FPN II Fund, the "Flagship Funds"). (xiii) Flagship VentureLabs VI Manager LLC ("VentureLabs VI Manager" and together with Flagship Fund VI GP, Flagship Fund VII GP, Nutritional LTP GP, Flagship Opportunities Fund II GP and FPN GP, the "Flagship GPs"). (xiv) Flagship Pioneering, LLC ("Flagship Pioneering"). (xv) Noubar B. Afeyan, Ph.D. ("Dr. Afeyan"). The address of the principal business office of each of the Reporting Persons is: c/o Flagship Pioneering 55 Cambridge Parkway, Suite 800E Cambridge, Massachusetts 02142 (i) Flagship Fund VI: Delaware (ii) Flagship Fund VI GP: Delaware (iii) PM02: Delaware (iv) Flagship Fund VII: Delaware (v) Flagship Fund VII GP: Delaware (vi) Nutritional LTP: Delaware (vii) Nutritional LTP GP: Delaware (viii) Flagship Opportunities Fund II: Delaware (ix) Flagship Opportunities Fund II GP: Delaware (x) FPN II Fund: Ontario, Canada (xi) FPN GP: Delaware (xii) VentureLabs VI: Delaware (xiii) VentureLabs VI Manager: Delaware (xiv) Flagship Pioneering: Delaware (xv) Dr. Afeyan: United States Y The information required by this item with respect to each Reporting Person is set forth in Rows 5 through 9 and 11 of the cover page to this Schedule 13G. The ownership percentages reported are based on 128,192,484 shares of Common Stock outstanding as of March 31, 2026, as reported by the Issuer in its Quarterly Report on Form 10-Q filed on May 7, 2026. Flagship Fund VI GP is the general partner of Flagship Fund VI and may be deemed to beneficially own the shares held directly by Flagship Fund VI. Flagship Fund VII is the majority equity holder of PM02 and may be deemed to beneficially own the shares held directly by PM02. Charles R. Carelli, Jr., Chief Financial Officer of Flagship Pioneering, is the sole manager of PM02. Flagship Fund VII GP is the general partner of Flagship Fund VII and may be deemed to beneficially own the shares held directly by each of PM02 and Flagship Fund VII. Nutritional LTP GP is the general partner of Nutritional LTP and may be deemed to beneficially own the shares held directly Nutritional LTP. Flagship Opportunities Fund II GP is the general partner of Flagship Opportunities Fund II and may be deemed to beneficially own the shares held directly by Flagship Opportunities Fund II. FPN GP is the general partner of FPN II Fund and may be deemed to beneficially own the shares held directly by FPN II Fund. VentureLabs VI Manager is the manager of VentureLabs VI and may be deemed to beneficially own the shares held directly by VentureLabs VI. Flagship Pioneering, as the manager of each of the Flagship GPs, and Dr. Afeyan, as the ultimate control person of Flagship Pioneering, may each be deemed to beneficially own the shares held directly by the Flagship Funds. See Item 4(a). See Row 5 of cover page for each Reporting Person. See Row 6 of cover page for each Reporting Person. See Row 7 of cover page for each Reporting Person. See Row 8 of cover page for each Reporting Person. Y Y Y Y Y Y Flagship Pioneering Fund VI, L.P. /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship Pioneering Fund VI General Partner LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Pioneering Medicines 02, LLC /s/ Charles R. Carelli, Jr. 05/15/2026 Flagship Pioneering Fund VII, L.P. /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship Pioneering Fund VII General Partner LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Nutritional Health LTP Fund, L.P. /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Nutritional Health LTP Fund General Partner LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship Pioneering Special Opportunities Fund II, L.P. /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship Pioneering Special Opportunities Fund II General Partner LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 FPN II, L.P. /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 FPN General Partner LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship VentureLabs VI, LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship VentureLabs VI Manager LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Flagship Pioneering, LLC /s/ Noubar B. Afeyan, Ph.D. 05/15/2026 Afeyan Noubar /s/ Noubar B. Afeyan, Ph.D. 05/15/2026