The United States faces significant environmental burden to treat and transport ˜0.61 billion kg of defective tomatoes (culled tomatoes) every year. The present disclosure provides for the treatment and processing of culled tomatoes in microbial-electrochemical systems, using the microbial fuel cell as a model reactor. The fundamental differences between the long-term oxidative behavior of unprocessed culled tomatoes compared to the three readily soluble substrates (dextrose, acetate, and wastewater) are disclosed. AC electrochemical impedance spectroscopy (EIS) analyses indicate the influential impedance contributions of the peel & seed to the cull oxidation. Cyclic voltammetry tests indicate that the indigenous redox-active pigments in the cull influence the faradaic processes involved in the cull oxidation.