Bioelectrochemical systems (BESs) are versatile electrochemical technologies that use microbial catalysts for simultaneously harvesting energy and treating wastewater. However, there is a consensus that practical energy applications and clean water production remain technically challenging for stand-alone BESs. To address these technological challenges, membrane-based technologies for water/wastewater treatment and energy production, such as electrodialysis, forward osmosis, reverse electrodialysis, and pressurized filtration (e.g., ultrafiltration), have been integrated into BESs. This integration has created new systems including microbial desalination cells, osmotic microbial fuel cells, pressurized filtration-microbial fuel cells, and microbial reverse-electrodialysis cells. This article aims to provide a comprehensive review on the recent progress in BESs integrated with membrane-based technologies, discuss advantages and limitations, and present outlooks toward further development of these technologies.