The primary production of coffee involves the extensive use of water resources, since it is not only used for irrigation of coffee plantations, but it is also required in large volumes for the processing of the coffee berry to obtain high quality green beans. It is calculated that for every kg of dry coffee grain produced, up to 40 L of water are consumed, and its disposal represents a significant environmental problem, since most coffee growers are small producers with no access to efficient technologies for wastewater treatment. This situation leads to these liquid wastes to be discarded untreated in natural water sources, generating environmental pollution and public health problems. Bioelectrochemical Systems (BES) have been proposed as an alternative to conventional wastewater treatments, either as a primary bioremediation strategy or for secondary wastewater treatment systems. Among BES, microbial fuel cells (MFCs) are designed to exploit the metabolic capability of andophilic microorganisms to degrade the organic matter present in the waste. Anodophilic microorganisms use electrodes as terminal electron acceptors, generating a flow of electrons that can be used in the generation of electricity. In this work, we evaluated the ability of native microbial communities to degrade the organic matter present in wastewater from the coffee agroindustry and its electrogenic potential for the co-generation of electricity was evaluated using an MFC device developed by the authors. Wastewater samples obtained at different stages of the coffee wet process were used as inoculum and feedstocks. The system was operated in fed-batch, in both open and closed-circuit conditions, for 60 days. The degree of decontamination or bioremediation of the wastewater was assessed by measurements of physicochemical parameters. For the characterization of the native microbial community, microscopic and molecular techniques were used and the electrogenic potential was established by assessing the electrochemical performance of the system. With the proposed bioelectrochemical system, a reduction of up to 70% of the initial content of organic matter of the residual water from the coffee benefit was achieved, and open circuit voltages of up to 400 mV were recorded, comparable to those reported for conventional air breathing cathode MFC.