Water quality deterioration caused by a wide variety of persistent organic pollutants (POPs) has become a serious concern worldwide. Traditional advanced oxidation process (e.g., Fenton reaction) is often inadequate, unsafe, and require post-treatment to remove residual H2O2. In this context, the bioelectrochemical technology assisted advanced oxidation reactions (namely bio-electro-Fenton system) have found a niche where they can become dominant in the near future, especially for POPs removal. Compared to traditional Electro-Fenton technologies, the bio-electro-Fenton system greatly reduced the expenses on wastewater treatment in terms of electric energy consumption and operation costs. The bio-electro-Fenton system is becoming a versatile platform technology and offers a new solution for emerging environmental issues related to wastewater treatment. This paper critically reviews the existing literature about the degradation of POPs in bio-electro-Fenton system, especially with respect to the treatment performance associated with reactor design and main operating parameters. The review aims to assist researchers and engineers to gain fundamental understandings and critical view of bio-electro-Fenton system, and hopefully with the knowledge it could bring new opportunities for the future development of this promising wastewater treatment technology.