Microbial fuel cells (MFC) can be a potential technique to harvest energy from waste organic biomass. Organic waste is a good source of carbon in the form of simple and complex polysaccharides. In this study, newspaper powder, dried dead microalgae biomass and mixed fruit peel powder were separately targeted as substrate for the growth of an isolated cellulolytic bacteria inside the anode chamber of three different MFCs. At cathode, bold basal medium with spent engine oil was used as catholyte. An isolated and acclimatized microalgae was used as cathode biocatalyst in order to perform bioremediation of spent engine oil wastewater at cathode chamber. The MFC with newspaper powder showed highest maximum power density of 34.88 ± 1.00 mW/m2. Both fruit peel powder and dried microalgae powder-based MFCs achieved almost parallel maximum power densities of 15.57 ± 0.49 mW/m2 (at 161.1 ± 2.54 mA/m2) and 16.00 ± 0.32 (at 163.3 ± 1.66 mA/m2), respectively. The anode chambers of all MFCs reflected chemical oxygen demand (COD) removal efficiencies in range of 65–86 %. At anode chamber, maximum COD removal of 86.25 % was achieved by microalgae powder based MFC. The removal percentage of oil and grease at cathode chamber were 37.7 %, 42.3 % and 29.1 % for fruit peel, newspaper powder and microalgae powder based MFCs respectively. Up to 76–80 % nitrate-nitrogen, 96–97 % ammonium-nitrogen, 90–94 % phosphate-phosphorous removal were observed at cathode chamber in all the MFCs. Microbial community analysis revealed that Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla present in all the three anodic biofilms.