Recalcitrant wastes including dyes, pesticides, explosives, heavy metals, polyalcohols, furan derivatives and phenolic substances, are of special concern owing to their recalcitrance and persistence in the environment. Bioelectrochemical systems (BESs) including microbial fuel cells (MFCs) and microbial electrolysis cells (MECs), integrate three important wastewater treatment options, namely, biological treatment, electrolytic dissociation and electrochemical oxidation/reduction, and are regarded as a new sustainable and effective strategy for treatment of these wastes. The simultaneous and cooperative roles of these multiple units running in parallel in BESs contribute to the efficiency of recalcitrant waste treatment, while substrate metabolism is considered to be a key step triggering different unit operations. An up-to-date review is provided on recent research and development in BESs-based recalcitrant wastes treatment. MFCs and MECs, as two types of BESs, are summarized in terms of treatment efficiency, recalcitrant substance metabolic pathway and microorganism diversity after a brief introduction to the electrochemical process for recalcitrant waste treatment. The scientific and technical challenges that have yet to be faced in the future are also discussed.