Microbial fuel cells (MFCs) are an alternative to conventional wastewater treatments that allow for the removal of organic matter and cogeneration of electrical energy, taking advantage of the oxidation–reduction metabolism of organic compounds conducted by microorganisms. In this study, the electrogenic potential and the capacity for the reduction of the organic matter of native microbial communities in wastewater from the wet processing of coffee were evaluated using open-cathode MFCs. To determine the electrogenic potential, a factorial experimental design was proposed in which the origin of the residual water and the source of the inoculum were evaluated as factors. The MFCs operated for 21 days in both open-circuit and closed-circuit operation modes. Voltage records, current determinations, and chemical oxygen demand (COD) analyses were used to establish the power reached in the electrochemical system and the degree of the decontamination of the wastewater. During the MFC operation, voltages from 200–400 mV and power and current densities from 300–900 mW·m−2 and 10–22 mA·m−2, respectively, were reached. The inoculum used, with a statistical significance of α < 0.05, influenced the electrogenic performance of the microbial fuel cell. The previous process of adaptation to the operational conditions of the MFCs of the native microbial community positively influenced the current generation in the system. The degradation rates reached 500–600 mg·L−1·day−1, indicating the metabolic capacity of the microbial community in the MFCs to achieve the decontamination of wastewater from the coffee agroindustry. It was shown the implementation of bioelectrochemical systems constituted a viable option for the treatment of agricultural waste in Colombia. In addition, it was observed the capacity to cogenerate electrical energy from the biotransformation of the polluting organic matter in the effluents of the coffee industry.