Microbial Fuel Cells (MFCs) are considered to be an environmental friendly energy conversion technology. The main limitations that delay their industrialization include low current and power densities achievable and long start-up times. Maximum Power Point Tracking (MPPT) has been proposed as a method to enhance MFCs electrical performances. However, the specialized literature is still lacking of experimental works on scaled-up reactors and/or real wastewater utilization. This study evaluates the impact of a MPPT system applied to MFCs treating swine wastewater in terms of start-up time and long-term performance. For this purpose, two replicate cells were compared, one with applied MPPT control and one working with fixed resistance. Both MFCs were continuously fed with swine wastewater to validate the control system under real and dynamic conditions. The study demonstrated that the automatic resistance control was able to reduce the start-up time of about one month. Moreover, MPPT system increased of 40% the Coulombic efficiency at steady-state conditions, reduced energy losses associated with anode and cathode reactions and limited methanogenic activity in the anode chamber. A power density of 5.0 ± 0.2 W m-3 NAC was achieved feeding the system at an Organic Loading Rate of 10 kg COD m-3 d-1.