Effluent from anaerobic membrane bioreactor (AnMBR) contains ammonia and would require post-polishing treatment before it can be disinfected by chlorine. However, additional post-treatment steps to remove nutrients offset the energetic benefits derived from anaerobic fermentation. The use of chlorine or ozone also promotes concerns associated with disinfection byproducts. This study evaluates UV/H2O2 as a potential strategy suited for the removal of pharmaceutical compounds as well as antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from AnMBR effluent. Our findings indicate that 10 mg/L H2O2 and 61.5 mJ/cm2 of UV fluence are able to achieve a 4-log removal of both Escherichia coli PI7 and Klebsiella pneumoniae L7. However, a higher fluence of 311 mJ/cm2 with the same amount of H2O2 would be required to achieve > 90% removal of atenolol, carbamazepine and estrone. The removal of the pharmaceutical compounds was driven by the hydroxyl radicals generated from H2O2, while UV exposure governed the inactivation of ARB and ARGs. UV/H2O2 increased overall mutagenicity of the treated wastewater matrix but did not result in any changes to the natural transformation rates. Instead, UV significantly reduced natural transformation rates by means of DNA damage. Overall, UV/H2O2 could be the ideal final disinfection strategy for AnMBR effluent without requiring additional post-treatment prior disinfection.