In this research, the effects of external resistance on the community structure and performance of mixed-culture microbial fuel cells (MFCs) were investigated. For the experiments, bench-scale flow-through MFCs were inoculated with anaerobic digester sludge and supplied with a mixture of acetate, propionate, butyrate, and lactate as electron donor. Potassium ferricyanide served as the electron acceptor in the cathodic chamber. After steady state was reached, non-destructive electrochemical analyses including cyclic voltammetry were conducted. At the end of the experiment, destructive analyses of the biofilm on the carbon cloth anode were performed including examination via scanning electron microscopy, measurement of protein content and DNA extraction for community analysis. The results suggest that the applied external resistance has a significant impact on the performance (i.e. power production), electrochemical characteristics, and community structure of MFCs.