Microbial fuel cells (MFC) and membrane bioreactors (MBR) are promising technologies for wastewater treatment. However, both of them have some drawbacks and application limitations. A cost-effective hybrid system (EMBR) integrating MFC with MBR was evaluated in terms of treatment performance and membrane fouling. In this paper, two electric field directions with a membrane module in the middle were applied to explore the mechanism of membrane fouling mitigation in EMBRs. In both configurations of EMBRs, microbial activity and degradation ability of activated sludge for chemical oxygen demand and NH4+−N removals could be enhanced compared with those for the controlled MBR. In addition, the irreversible resistance significantly decreased, especially in the EMBR(−) with a longer operation time. Furthermore, two critical factors, namely enhanced bioflocculation and electrophoresis forces, were compared based on key parameters (zeta potential, particle size distribution and extracellular polymeric substances). The electrophoresis forces made a greater contribution to fouling alleviation than that conducted by the enhanced bioflocculation. The results suggested that EMBR, as a promising wastewater treatment technology, improved effluent quality and reduced energy consumption.