Bioelectrochemical systems take advantage of the capacity of certain bacteria to exchange electrons with an external electrode. Among the many applications that use this biological mechanism, Microbial Fuel Cells (MFCs) are increasingly being studied as an alternative or complementary technology for wastewater treatment with simultaneous generation of an electrical current. In this work the influence of a series of parameters (anode material, current, cathodic catalysts and operational temperature) on the performance of a specific MFC has been investigated. Water composition, microbial community diversity and electrochemical response have been analyze. Anodic material and flow of current proved to select for different bacterial communities. MFCs were better than conventional anaerobic digesters in carrying out pollutants removal at low temperatures, and generated electricity in the range of 10 to 4ºC. Low cost non-noble catalysts for oxygen reduction met the requirements for the cathode in the MFCs tested, at a performance level comparable to platinum.