As the bioelectrochemical system, the microbial fuel cell (MFC) and the microbial electrolysis cell (MEC) were developed to selectively recover Cu²⁺ and Ni²⁺ ions from wastewater. The wastewater was treated in the cathode chambers of the system, in which Cu²⁺ and Ni²⁺ ions were removed by using the MFC and the MEC, respectively. At an initial Cu²⁺ concentration of 500 mg·L^-1, removal efficiencies of Cu²⁺ increased from 97.0%±1.8% to 99.0%±0.3% with the initial Ni²⁺ concentrations from 250 to 1000 mg·L^-1, and maximum power densities increased from 3.1±0.5 to 5.4±0.6 W·m^-3. The Ni²⁺ removal mass in the MEC increased from 6.8±0.2 to 20.5±1.5 mg with the increase of Ni²⁺ concentrations. At an initial Ni²⁺ concentration of 500 mg·L^-1, Cu²⁺ removal efficiencies decreased from 99.1%±0.3% to 74.2%±3.8% with the initial Cu²⁺ concentrations from 250 to 1000 mg·L^-1, and maximum power densities increased from 3.0±0.1 to 6.3±1.2 W·m^-3. Subsequently, the Ni²⁺ removal efficiencies decreased from 96.9%±3.1% to 73.3%±5.4%. The results clearly demonstrated the feasibility of selective recovery of Cu²⁺ and Ni²⁺ from the wastewater using the bioelectrochemical system.