At least 50% of the wastewater from human activities is discharged into the environment without treatment, a practice that compromises the human right to access clean water and sanitation. Microbial fuel cells (MFCs) are devices capable of converting chemical energy into electrical energy through electrochemical reactions, using the electrosynthesis of microorganisms. In this work, a device composed of two chambers is proposed. Biodigester effluent is used as an anolyte and oxidation of organic components is perfomed by bacteria at the electrode surface in the anodic chamber, while the reduction of heavy metals from industrial wastewater takes place in the cathodic chamber. The proposed MFC can simultaneously reduce the load of pollutants in agricultural and metallurgic wastewater and produce renewable energy. The objective of this study is to determine the effect of coating the graphite electrodes in the cathodic and anodic chamber with carbon nanomaterials, including graphene and a seamless hybrid of graphene and carbon nanotubes, both materials obtained by chemical vapour deposition. The nanostructured electrodes provide a larger surface area and increased electron transfer rates to improve the performance of bioelectricity generation. This work improves the comprehension of bioelectrochemical phenomena occurring in biofilm-based microbial devices and analyzes how the electrode surface structure can tune the charge transfer efficiency at the interface of living organism and carbon electrodes.