•High collaborative efficiency for both organics and Cu2+ removal was achieved.•High anodic and cathodic efficiencies and high power densities were achieved under the optimal operation parameters.•The optimal operation parameters were determined by linear sweep voltammetry. Organic matters and copper ions can be collaboratively removed from wastewater using a microbial fuel cell (MFC). High collaborative efficiencies for both organic matter and copper ions removal have not been achieved yet in previous studies. We demonstrate here that high collaborative efficiencies can be achieved by designing reactor construction and selecting operational parameters based on the results of linear sweep voltammetry (LSV). When the MFC was constructed as 1:2 volume ratio of anode to cathode chamber and operated at optimal conditions, 83% COD removal and 87% copper ion removal were obtained at the same time. In addition, the Cu-MFC also performed a high coulombic efficiency (CE) of 89% for organic treatment, a cathodic efficiency of 80% for copper ion removal, and a maximum power density of 2.0W/m2.