Microbial fuel cells (MFCs) are a promising technology that generates electricity from several biodegradable substrates and wastes. The main drawback of these devices is the need of using a catalyst for the oxygen reduction reaction at the cathode, which makes the process relatively expensive. In this work, two low cost materials are tested as catalysts in MFCs. A novel iron complex based on the ligand n-phenyledenparaethoxy aniline has been synthesized and its performance as catalyst in single chamber MFCs containing ionic liquids has been compared with a commercial inorganic material such as Raney nickel. The results show that both materials are suitable for bioenergy production and wastewater treatment in the systems. Raney nickel cathodes allow MFCs to reach a maximum power output of 160 mW.m−3 anode, while the iron complex offers lower values. Regarding the wastewater treatment capacity, MFCs working with Raney nickel-based cathodes reach higher values of chemical oxygen demand removal (76%) compared with the performance displayed by the cathodes based on Fe-complex (56%).