Microbial energy generation systems, i.e., bioelectrochemical systems (BESs) are promising sustainable technologies that have been used in different fields of application such as biofuel production, biosensor, nutrient recovery, wastewater treatment, and heavy metals removal. However, BESs face great challenges such as large-scale application in real time, low power performance, and suitable materials for their configuration. This review paper aimed to discuss the use of BES systems such as conventional microbial fuel cells (MFCs), as well as plant microbial fuel cell (P-MFC), sediment microbial fuel cell (S-MFC), constructed wetland microbial fuel cell (CW-MFC), osmotic microbial fuel cell (OsMFC), photo-bioelectrochemical fuel cell (PBFC), and MFC-Fenton systems in the zero waste sustainable recovery process. Firstly, the configuration and electrode materials used in BESs as the main sources to improve the performance of these technologies are discussed. Additionally, zero waste recovery process from solid and wastewater feedstock, i.e., energy recovery: electricity generation (from 12 to 26,680 mW m-2) and fuel generation, i.e., H2 (170 ± 2.7 L-1 L-1 d-1) and CH4 (107.6 ± 3.2 mL-1 g-1), nutrient recovery of 100% (PO43-P), and 13-99% (NH4+-N), heavy metal removal/recovery: water recovery, nitrate (100%), sulfate (53-99%), and sulfide recovery/removal (99%), antibiotic, dye removal, and other product recovery are critically analyzed in this review paper. Finally, the perspective and challenges, and future outlook are highlighted. There is no doubt that BES technologies are an economical option for the simultaneous zero waste elimination and energy recovery. However, more research is required to carry out the large-scale application of BES, as well as their commercialization.