A three-tank microbial fuel cell (MFC) is successfully constructed to achieve electromigration and is used in the electro-Fenton process to treat bisphenol A (BPA). The MFC system exhibits excellent mobility and efficiently aggregates Cu+ to the cathode. Under optimal operating conditions, the MFC achieves a maximum power density of 31.4 mW/m2, which is a 3.4-fold increase over that at 0.5 kΩ. Increasing the external resistance increased the MFC power output (ca 1.5 times) and copper ion migration (ca 4.6 times) while reducing the internal resistance of the system (ca 25.3 %). Surface analysis of the cathode carbon cloth shows a 5.5-fold increase in copper content at 1 kΩ over that at 0.5 kΩ. This also increases the oxygen reduction reaction rate, thereby increasing the H2O2 yield by 1.5 times. The recovered copper cathode at 1 kΩ exhibits the best catalytic degradation of BPA, removing 99.7 % of BPA in 180 min, increasing 1.4 and 1.8 times that obtained at 1.5 and 0.5 kΩ, respectively. The optimal operating conditions significantly increased the abundance of electrochemically active bacteria (Azospirillaceae) (3.2 %−41.7 %), indicating that the optimized MFC is favorable for the rapid acclimatization of electrochemically active bacteria.