Electrically conductive, graphene-coated, hollow-fiber porous membranes were used as cathodes in anaerobic electrochemical membrane bioreactors (AnEMBRs) operated at different applied voltages (0.7 and 0.9 V) using a new rectangular reactor configuration compared to a previous tubular design (0.7 V). The onset of biofouling was delayed and minimized in rectangular reactors operated at 0.9 V compared to those at 0.7 V due to higher rates of hydrogen production. Maximum transmembrane pressures for the rectangular reactor were only 0.10 bar (0.7 V) or 0.05 bar (0.9 V) after 56 days of operation compared to 0.46 bar (0.7 V) for the tubular reactor after 52 days. The thickness of the membrane biofouling layer was approximately 0.4 μm for rectangular reactors and 4 μm for the tubular reactor. Higher permeate quality (TSS = 0.05 mg/L) was achieved in the rectangular AnEMBR than that in the tubular AnEMBR (TSS = 17 mg/L), likely due to higher current densities that minimized the accumulation of cells in suspension. These results show that the new rectangular reactor design, which had increased rates of hydrogen production, successfully delayed the onset of cathode biofouling and improved reactor performance.