Increasing demand for renewable energy in the backdrop of global change calls for waste valorization and circular economy strategies. Public health concerns and demand for clean energy provide impetus to the development of wastewater based MFC. Wastewater treatment and simultaneous generation of bioelectricity offer a myriad of environmental benefits. Nevertheless, it is pertinent to know the challenges with the microbial fuel cell (MFC) technology to upscale the wastewater based MFC. This paper attempts to critically analyse the processes, application, challenges and opportunities of wastewater based MFCs. A literature survey was conducted to find out the advances in the field of wastewater based MFCs and the focus was to decipher the challenges to the implementation of wastewater based MFCs. Recent developments in MFC technology have improved the power output and studies show that a diverse group of organic-rich wastewater can be treated with MFCs. The developments include improvements in MFC configuration, development of biocatalysts and biocathode, anodic biofilm formation, microbial community interactions, and progress in the organic and pollutant removal. Nevertheless, the MFC technology is replete with challenges about the organic removal rate, power density, electrode performance limiting factors, economic viability, high initial and maintenance cost and difficulty to maintain the exoelectrogens activity in a complex wastewater environment. Opportunities exist in scaling up of MFCs, integration with other wastewater treatment methods and measures to minimise the operating costs. MFCs have the potential to increase the resilience capacity of the sustainable wastewater treatment plant.