Bioelectrochemical systems (BES) are commonly utilized to generate green electricity, chemicals, and materials through bioelectrocatalytic processes. Over the years, the growing interests in low carbon energy, wastes valorization and the sustainable bioremediation of environmental pollutants have generated interests in BES such as microbial fuel cells (MFC) and bioelectrochemical fuel cells (BFC). The MFCs are the most advanced BES that can ensure the microbial conversion of chemical energy into electrical energy. Therefore, this article seeks to review and present valuable literature on the fundamental operational principles, mechanisms and understanding of BES such as MFCs. It seeks to highlight the schematics of these systems along with the processes and mechanisms such as the oxidation of organic substrates ranging from acetate compounds to complex mixtures. Furthermore, the prospects, challenges, and future applications of BES technologies are presented. The findings indicate that BFCs and MFCs are hampered by low efficiencies, energy output, mass transfer, porosity, and proton conductivity of the electrode and membrane materials along with mechanical strength, scalability, biocompatibility, and chemical stability. However, BES could potentially impact on clean energy production, greenhouse gases mitigation, wastewater treatment, bioanalysis, biosensors, and environmental remediation in the future.