Anaerobic co-digesters are biorefineries for energy recovery from food waste and domestic wastewater via methane production. Nonetheless, the performance of this technology was not always satisfied due to the long chain fatty acids (LCFAs) generation from food waste. Micronutrient supplementation is an effective strategy that could be applied during the anaerobic (co-)digestion to further enhance the digestion efficiency while treating food waste. In this study, supplementing copper (as CuSO and CuCl ) at 10, 30, and 50 mg/L Cu was selected to further enhance the methane production of anaerobic co-digester while treating food waste and domestic wastewater. Overall, with the supplementation of copper, the chemical oxygen demand (COD) removal efficiency was over 90%, while higher methane yields (0.260–0.325 L CH /g COD ) were obtained compared to the control without supplementation (0.175 L CH /g COD ). For the cumulative methane yield, the highest increment of 94.1% was obtained when 10 mg/L of Cu were added. The results showed copper as a cofactor of many microbial enzymes and coenzymes involved in the methane production further improved both methane production and COD removal efficiency. Meanwhile, the microbial community analysis verified the copper supplementation significantly changed the bacterial communities but with the limited effect on the diversity of archaea. Furthermore, since the anaerobic co-digester was not that much efficient on the nutrients removal, the effluent from the upflow anaerobic sludge blanket (UASB) reactor was further treated by the anaerobic/anoxic/oxic (A O) rector and the resulting effluent reached the satisfying quality in terms of COD, total nitrogen (TN), and NH -N removal, meeting the regional effluent discharge limits.