Environmental pollution and energy are interlinked; thereby an integrated approach is needed based on intra- and cross-disciplinary solutions. Microbial electro-Fenton, an innovative form of microbial electrochemical technologies, is an essential approach in this regard, which couples waste bioremediation and pollutant removal simultaneously from anode and cathode chambers with bioelectricity production. This article reviews the application of microbial electro-Fenton systems for environmental remediation and clean energy generation. Recent advances in fabrication of electrode materials to increase anodic biocompatibility and cathodic oxygen reduction reaction, cell design/configuration, membranes/separators and iron species as Fenton catalysts are discussed in detail. In addition, contemporary developments in the application of microbial electro-Fenton systems to deal with real wastewaters, wide variety of industrial pollutants and various classes of emerging contaminants are elucidated. Furthermore, the limitations and future perspectives are pointed out in detail. We believe that this in-depth review may aid as a reference guide for environmental scientists working on microbial electro-Fenton system.