One of the most advanced systems of microbial fuel cells is the benthic microbial fuel cell (BMFC). Despite several developments, this strategy still has a number of significant flaws, such as instable organic substrate. Waste material (sugarcane) is used as a substrate in this work to address the organic substrate instability. The process was operated continuously for 70 days. A level of 300 mV was achieved after 33 days of operation, while the degradation efficiencies of Pb (II), Cd (II), and Cr (III) were more than 90%. More than 90% of the removed chemical oxygen demand (COD) was also recorded. The measured power density was 3.571 mW/m2 at 1000 external resistance with 458 internal resistance. This demonstrates that electrons are effectively transported throughout the operation. The Bacillus strains are the most dominant bacterial community on the surface of the anode. This research’s mechanism, which involves metal ion degradation, is also explained. Finally, parameter optimization indicated that pH 7 works efficiently. In addition to that, there are some future perspectives and concluding remarks enclosed.