[4][5] Committee Chairman Jack Reed (D‑RI) initially voted against the bill, due to disagreement with the decision to increase defense spending $25 billion over the budget cap established by the Fiscal Responsibility Act; Elizabeth Warren (D‑MA) and Tom Cotton (R‑AR) joined Reed in voting against the bill.

Many Democrats criticized the changes and the House Republicans for using the mandatory defense bill to push forward divisive, partisan agendas.

The amendments would block funding to gender-affirming care for transgender members of the United States Armed Forces,[4] for military diversity, equity, and inclusion programs,[4] for teaching of critical race theory at military academies, climate change efforts, and for any future efforts to help bring Palestinian refugees to the United States.

[8] On July 8, the Senate Armed Services Committee publicly released its version of the NDAA text,[9] which was revealed to include a provision restricting gender-affirming care in the military, approved by a vote of the Republican members of the Committee with the support of conservative Democratic Senator Joe Manchin.

[10] In July 2024, a coalition of industry groups authored a joint letter to members of both the House Armed Services Committee and Senate Armed Services Committee opposing Section 828 of the Senate version of the Act (S. 4638), entitled "Requirement for Contractors to Provide Reasonable Access to Repair Materials," which would require contractors doing business with the US military to agree "to provide the Department of Defense fair and reasonable access to all the repair materials, including parts, tools, and information, used by the manufacturer or provider or their authorized partners to diagnose, maintain, or repair the good or service.

[12] In November 2024, it was reported that Senate Majority Leader Chuck Schumer (D‑NY) wanted to attach the controversial Antisemitism Awareness Act, which the House had passed earlier in the year, to the 2025 NDAA.

[15] The version of the bill that was negotiated and agreed to by the House and Senate removed provisions that restricted abortion access, DEI programs and gender-affirming care for active-duty service members.

[26] LGBTQ Nation said that, due to the vague language of the provision, which bans TRICARE coverage of gender dysphoria "treatments that could result in sterilization" for minors, but does not name any specific treatments, it is unclear if the provision will actually be able to ban TRICARE coverage of gender-affirming care for minors since puberty-blocking drugs do not affect fertility.

[30][31] On December 23, 2024, Biden signed the bill into law, but issued a statement saying he "strongly opposes" the provision restricting coverage of gender-affirming treatments for minors under TRICARE.