A novel bioelectrochemical system (BES) was designed to recover copper and nickel from wastewater sequentially. The BES has two chambers separated by a bipolar membrane and two cathodes. Firstly, the copper ions were reduced on a graphite cathode with electricity output, and then with an additional bias-potential applied, the nickel ions were recovered sequentially on a copper sheet with electricity input. In this design, nickel and copper can be recovered and separated sequentially on two cathodes. By adjusting the molar ratio of copper and nickel ions to 2.99:1 in wastewater, 1.40 mmol Cu2+ could be recovered with 143.78 J electricity outputs, while 50.68 J electricity was input for 0.32 mmol nickel reduction. The total energy output of copper recovery was far more than the electricity input of nickel reduction. The present technology provides a potential method for heavy metal ion separation and recovery.