Audit the Pentagon Act of 2021 This bill requires defense spending reductions during any fiscal year after FY2022 where the Comptroller of the Department of Defense (DOD) fails to certify that a department, agency, or other element of DOD has achieved an unqualified opinion on its full financial statements. The amount of any reductions must be deposited in the General Fund of the Department of the Treasury and must be available for deficit reduction. The bill excludes from any reductions accounts related to military personnel, reserve personnel, National Guard personnel, and the Defense Health Program. The President may waive a reduction if the President certifies that a reduction would negatively affect (1) national security or members of the Armed Forces who are deployed in combat zones, or (2) the Defense Health Program account.