In this study, microbial fuel cells (MFCs) - operated with novel cation- and anion-exchange membranes, in particular AN-VPA 60 (CEM) and PSEBS DABCO (AEM) - were assessed comparatively with Nafion proton exchange membrane (PEM). The process characterization involved versatile electrochemical (polarization, electrochemical impedance spectroscopy - EIS, cyclic voltammetry - CV) and biological (microbial structure analysis) methods in order to reveal the influence of membrane-type during start-up. In fact, the use of AEM led to 2-5 times higher energy yields than CEM and PEM and the lowest MFC internal resistance (148 +/- 17 Omega) by the end of start-up. Regardless of the membrane-type, Geobacter was dominantly enriched on all anodes. Besides, CV and EIS measurements implied higher anode surface coverage of redox compounds for MFCs and lower membrane resistance with AEM, respectively. As a result, AEM based on PSEBS DABCO could be found as a promising material to substitute Nafion.