Lack of process control between the two stages of a combined microbial fuel cell-membrane bioreactor (MFC-MBR) system limits its application in wastewater treatment due to membrane fouling and high energy consumption. In this study, a two-stage MFC-MBR integrated system was established to investigate the impact of incorporating process control on petroleum refinery wastewater treatment. The results showed that chemical oxygen demand (COD) removal exhibits a linear relationship with the MFC voltage output (R2 = 0.9821); therefore, the MFC was used as a biosensor to control the combined system. The removal efficiencies of COD, ammonium nitrogen (NH4+-N), and total nitrogen (TN) were 96.3%, 92.4%, and 86.6%, respectively, in the MFC-MBR biosensor, whereas those in the control system were 74.7%, 71.2%, and 64.7% respectively. Furthermore,using the biosensor control system yielded a 50% reduction in the transmembrane pressure (1.01 kPa day−1) and decreased membrane fouling in wastewater treatment. The maximum energy recovery of the biosensor system (0.00258 kWh m−3) was five times higher than that of the control system, as determined by calculating the mass balance of the system. Thus, this study indicates that using the MFC as a biosensor for process control in an MFC-MBR system can improve overall system performance. © 2021 Elsevier Inc.