Microbial fuel cells (MFCs) have shown great advantages in electricity production, heavy metal removal, and energy recovery. However, the impact and mechanism of conflicting effects of numerous electron acceptors on heavy metal removal remain unknown. The effects of different initial heavy metal concentrations, cathodic dissolved oxygen, and electrode materials on the electricity generation and heavy metal removal efficiencies of Cu(II) and Cr(VI) were investigated in this study. When the initial concentration of Cr(VI) increased from 10 mg/L to 150 mg/L, the maximum voltage, coulomb efficiency, and maximum power density declined from 99 to 44 mV, 28.63% to 18.97%, and 14.29 to 0.62 mW/m2, and the removal efficiencies of Cu(II) and Cr(VI) decreased dramatically from 98.34% and 99.92% to 67.09% and 37.06%, respectively. Under anaerobic cathodic conditions, the removal efficiency and removal rate of Cu(II) and Cr(VI) were lower than those under aerobic conditions. When the cathode electrode was titanium sheet and graphite plate, the coulomb efficiency and maximum power density increased to 38.18%, 50.71%, 33.95 mW/m2, and 62.23 mW/m2. The removal efficiency and removal rates of Cu(II) and Cr(VI) were significantly increased to 98.09%, 86.13%, and 0.47, 0.50 mg/(L h) with a graphite plate, respectively. The pH of the cathode varied considerably greater as the MFC current increased. Cu(II) and Cr(VI) were removed and reduced to elemental Cu, Cu2O, and its oxides as well as Cr(OH)3 and Cr2O3 precipitates on the cathode electrode by cathodic bioelectrochemical reduction.