Industrial activity has resulted in heavy metals anthropogenic contamination of groundwater, especially in industrial or mining areas. Bioelectrochemical systems (BES) can be used for metals removal and recovery from aqueous solutions. In the framework of GREENER project, double-chamber BES have been adopted to treat groundwater from industrial sites containing copper, nickel and zinc (Cu, Ni and Zn), among other contaminants. Two operation modes, (i) short-circuited microbial fuel cell (MFC), and (ii) power supply driven microbial electrolysis cell (MEC, poisoning the cathode at -0.4 V vs. Ag/AgCl), were studied for metals removal at lab-scale. Two control reactors were run to evaluate metals adsorption on cathodes and membranes, and the effect of anolyte composition. Synthetic water containing different concentrations of Cu, Ni and Zn were treated, and metals removal pathways were studied. MEC and MFC performed similarly and the highest removal efficiencies were 97.1±3.6%, 50.7±6% and 74,5% for Cu, Ni and Zn respectively, from initial concentrations in the range of 1.1-1.5 mM.