Air-breathing cathode microbial fuel cells (MFCs) fed with citrus juice processing wastewater were employed for bioenergy production and simultaneously for wastewater treatment. Polymer inclusion membranes based on the ionic liquid methyltrioctylammonium chloride were tested as separator in this microbial fuel cell assembly. Regarding the wastewater treatment capacity, the evolution of the chemical oxygen demand (COD) removal over time reaches a maximum value of 45%. In addition to COD removal, an electrochemical characterization of the wastewater before and after being treated was also performed. Despite this type of feedstock not being ideal for bioenergy production in air-breathing cathode MFCs due to the acidity of the substrate, enough amount of bioenergy is produced to consider this technology a suitable alternative for reusing citrus juice processing wastewater.