In the present work, four different wastewaters from the food industry were used in parallel, in four identical dual-chamber MFCs, with graphite granules as anodic electrodes. Specifically, a mixture of hydrogenogenic reactor effluents (effluents from a dark fermentation reactor fed with cheese whey (CW), for hydrogen production), CW, and a mixture of expired fruit juices and wastewater from the confectionery industry were simultaneously used in MFCs to evaluate the effect of the type of effluent/wastewater on their efficiency. An electrochemical characterization was performed using electrochemical impedance spectroscopy measurements under open- (OCP) and closed-circuit conditions, at the beginning and end of the operating cycle, and the internal resistances were determined and compared. The results showed that the highest OCP value, as well as the highest power density (Pmax) and Coulombic efficiency (εcb) at the beginning of the operating cycle, was exhibited by the MFC, using a sugar-rich wastewater from the confectionery industry as substrate (sugar accounts for almost 92% of the organic content). This can be correlated with the low internal resistance extracted from the Nyquist plot at OCP. In contrast, the use of CW resulted in a lower performance in terms of OCP, εcb and Pmax, which could be correlated to the high internal resistance and the composition of CW, a substrate rich in lactose (disaccharide), and which also contains other substances (sugars account for almost 72% of its organic content, while the remaining 28% is made up of other soluble compounds).