High-energy consumption globally has raised questions about the low environmentally friendly and high-cost processes used until now for energy production. Microbial fuel cells (MFCs) may support alternative more economically and environmentally favorable ways of bioenergy production based on their advantage of using waste. MFCs work as bio-electrochemical devices that consume organic substrates in order for the electrogenic bacteria and/or enzyme cultures to produce electricity and simultaneously lower the environmental hazardous value of waste such as COD. The utilization of organic waste as fuels in MFCs has opened a new research path for testing a variety of by-products from several industry sectors. This review presents several organic waste substrates that can be employed as fuels in MFCs for bioenergy generation and the effect of their usage on power density, COD (chemical oxygen demand) removal, and Coulombic efficiency enhancement. Moreover, a demonstration and comparison of the different types of mixed waste regarding their efficiency for energy generation via MFCs are presented. Future perspectives for manufacturing and cost analysis plans can support scale-up processes fulfilling waste-treatment efficiency and energy-output densities.