A manganese oxide-coated cylindrical graphite cathode with a zinc anode was developed to treat wastewater containing selenite in a dual-chambered microbial fuel cell. COD and selenite removal in the anodic chamber by Bacillus cereus with energy generation were evaluated in batch mode. A manganese dioxide-coated graphite cathode was tested for its surface morphology and chemical composition using scanning electron microscopy and dispersive energy analysis of X-rays. Compared to the non-coated graphite electrode, up to 69% enhancement was observed in the manganese dioxide-coated electrode voltage generation with 150 ppm selenite concentration. The fuel cell achieved a maximum power density of 1.29 W/m2 with 91% selenite reduction and up to 74% COD (initial COD of 120 mg/L) removal for an initial selenite concentration from 100 to 150 ppm. The current study demonstrated the possibility of a modified cathode in enhancing energy generation and the use of microbial fuel cell technology to treat wastewater containing selenite.