Microbial fuel cells (MFCs) have been intensively studied at a bench scale and the further development of this technology requires system scaling up and understanding of their performance under non-laboratory conditions. In this study, a 200 L modularized MFC system consisting of 96 MFC modules was developed and operated in a local wastewater treatment plant for treating primary effluent. During more than 300 days' operation, the MFC system removed more than 75% of the total chemical oxygen demand and 90% of the suspended solids, despite significant fluctuations in treatment performance affected by wastewater quality and operational factors. It achieved 68% removal of ammonia nitrogen, but phosphorous and the nitrate accumulated due to nitrification needs further disposal. The frequency of the catholyte recirculation exerted a strong effect on the energy consumption of the MFC system. Through both parallel and serial electric connections, the MFC system generated power of ∼200 mW that was extracted by a power management system to drive a 60 W DC pump for catholyte recirculation. Over 60% of the material cost of the MFCs was due to the cation exchange membrane, and the capital cost of the MFC system could be comparable to that of small wastewater treatment facilities. The results of this study encourage the further development of MFC technology with reduced costs and improved performance towards sustainable wastewater treatment.