Using a CH[subscript 4]-based membrane biofilm reactor (MBfR), we studied perchlorate (ClO[subscript 4]–) reduction by a biofilm performing anaerobic methane oxidation coupled to denitrification (ANMO-D). We focused on the effects of nitrate (NO[subscript 3]–) and nitrite (NO[subscript 2]–) surface loadings on ClO[subscript 4]– reduction and on the biofilm community’s mechanism for ClO[subscript 4]– reduction. The ANMO-D biofilm reduced up to 5 mg/L of ClO[subscript 4]– to a nondetectable level using CH[subscript 4] as the only electron donor and carbon source when CH[subscript 4] delivery was not limiting; NO[subscript 3]– was completely reduced as well when its surface loading was ≤0.32 g N/m[superscript 2]-d. When CH[subscript 4] delivery was limiting, NO[subscript 3]– inhibited ClO[subscript 4]– reduction by competing for the scarce electron donor. NO[subscript 2]– inhibited ClO[subscript 4]– reduction when its surface loading was ≥0.10 g N/m[superscript 2]-d, probably because of cellular toxicity. Although Archaea were present through all stages, Bacteria dominated the ClO[subscript 4]–-reducing ANMO-D biofilm, and gene copies of the particulate methane mono-oxygenase (pMMO) correlated to the increase of respiratory gene copies. These pieces of evidence support that ClO[subscript 4]– reduction by the MBfR biofilm involved chlorite (ClO[subscript 2]–) dismutation to generate the O[subscript 2] needed as a cosubstrate for the mono-oxygenation of CH[subscript 4].