The effects of bulk- and nano-sized CuO and ZnO particles on biogas and methane production during anaerobic digestion of cattle manure were studied for a period of 14 days at 36 °C using the ISO 13641-2 guidelines. Biogas production was severely affected at concentrations of bulk and nanoparticles over 120 and 15 mg/L for CuO and 240 and 120 mg/L for ZnO, respectively. EC50 concentrations for methane inhibition were estimated to be 129 mg Cu/L for bulk CuO, 10.7 mg Cu/L for nano CuO, 101 mg Zn/L for bulk ZnO and 57.4 mg Zn/L for nano ZnO. The solubility of CuO nanoparticles in the reaction mixture was observed after 14 days of incubation and was significantly higher than the levels observed for ZnO. These results are of significant importance, as it is the first time that the effects of metal oxide particle size on biogas and methane production have been studied.