While the efficiency of microbial electrolysis cell (MEC) systems has improved remarkably, their application in continuous reactors and wastewater treatment remains poorly understood. This study evaluated the performance of a continuous-flow MEC using livestock wastewater and food waste as substrates. The MEC system achieved a hydrogen production rate of 5.2 L/L/day using acetate as a substrate, and a rate of 2.9–4.6 L/L/day when real wastewater mixtures were used. In terms of chemical oxygen demand (COD) removal, the system demonstrated high efficiency, with values ranging from 42.3 % to 62.2 % depending on the wastewater composition. Volatile fatty acid (VFA) removal reached up to 72.8 %. The current density averaged 9.9 A/m2 with acetate and decreased to 7.0 and 6.1 A/m2 in phases using wastewater, reflecting the adaptation of the microbial community to the more complex substrates. The microbial community was dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes, with Proteobacteria showing a particularly high abundance near the anion exchange membrane (AEM) on the anode. The MEC process demonstrates substantial promise as a sustainable technology for both biohydrogen production and wastewater treatment. With further optimization and scaling, MECs could play a crucial role in the circular economy by converting waste into clean energy while simultaneously treating wastewater, offering a pathway toward more sustainable industrial and environmental practices.