Fruit and vegetable wastes contain high amounts of organic matter, which allows the proliferation of a diverse range of bacterial communities, including fermentative, methanogenic, and acetogenic bacteria. Moreover, some microorganisms in these residues can oxidize complex organic compounds and generate electricity through electrochemical processes. Thus, this study aimed to identify electrochemically active bacteria derived from tomato crop residues, as these bacteria have great potential for application in emerging technologies, such as microbial fuel cells. For this purpose, a single-chamber microbial fuel cell (MFC) was constructed consisting of a rectangular polyethylene cube with two electrodes: zinc (cathode) and copper coated with activated carbon (anode). Liquid tomato paste (150 ml) was added and conditioned at 25 °C for 21 days. The maximum voltage was generated on day 13, reaching 0.85 V. The cells showed a pH range of 4.3–6.2 during the 21 days of monitoring. The Brix degree values decreased progressively from the initial value of 5° Brix. The microbial density comprised bacteria and yeasts, with the maximum bacteria count reaching 6.25 log CFU/g on day 11 and the maximum yeast count reaching 5.45 log CFU/g on day 9. Proteus vulgaris, Acinetobacter bereziniae, and Candida ciferrii were identified as microorganisms present in the energy generation of MFCs. In conclusion, the microorganisms present in tomato residues can generate energy, providing an alternative to adding value to waste, thereby reducing pollution and developing environmentally sustainable energy.