Microbial fuel cells (MFCs) have been presented as advanced engineered renewable technologies to convert the stored chemical energy in various contaminated organic sources into electric energy via bioelectrochemically active anodic biofilm (EAB) under strictly anaerobic conditions into carbon dioxide, electrons, and protons and then the resulted electrons moved to the cathode chamber for the occurrence of reduction process in the presence of oxygen to form water and to liberate the electric energy. Moreover, there are several factors that can influence the performance of MFCs, which include MFC configuration, cathode electrode materials and anode electrode materials, types of electron acceptor, microorganism interaction, biofilm structure, electron transfer mechanisms, source, external resistance, type and concentration of substrates. The present chapter aims to provide a comprehensive overview on the vital factors that affect the performance of MFCs. Additionally, the usage of these MFCs in the treatment of polluted wastewater through the bioremediation of the existence organic substrates to form bioelectricity, biohydrogen, methane production, and the removal of toxic compounds. Besides, MFCs can be used in remote used areas owing to their application as biosensors for producing sustainable bioenergy generation. The previous diverse applications of MFCs produce it as estimable technology for maintainable progress. Also, the implementation of MFCs face several limitations that reduce the power output, for examples, technological, microbiological, and economic challenges that should be eliminated before large-scale operations for enhancing the power generation. Furthermore, for MFCs sustainable commercialization, widespread researches must be studied and provided with funding in these areas for increasing the power output and hence, improving the efficiency of the MFCs batteries.