Bio-electro-Fenton (BEF) systems have been potentially studied as a promising technology to achieve environmental organic pollutants degradation and bioelectricity generation. The BEF systems are interesting and constantly expanding fields of science and technology. These emerging technologies, coupled with anodic microbial metabolisms and electrochemical Fenton’s reactions, are considered suitable alternatives. Recently, great attention has been paid to BEFs due to special features such as hydrogen peroxide generation, energy saving, high efficiency and energy production, that these features make BEFs outstanding compared with the existing technologies. Despite the advantages of this technology, there are still problems to consider including low production of current density, chemical requirement for pH adjustment, iron sludge formation due to the addition of iron catalysts and costly materials used. This review has described the general features of BEF system, and introduced some operational parameters affecting the performance of BEF system. In addition, the results of published researches about the degradation of persistent organic pollutants and real wastewaters treatment in BEF system are presented. Some challenges and possible future prospects such as suitable methods for improving current generation, selection of electrode materials, and methods for reducing iron residues and application over a wide pH range are also given. Thus, the present review mainly revealed that BEF system is an environmental friendly technology for integrated wastewater treatment and clean energy production.