In this study, microbial fuel cells deploying heterogeneous ion exchange membranes were assessed. The behavior of the cells as a function of the membrane applied was evaluated in terms of maximal current density, electron recovery efficiency and energy production rate (up to 427.5 mA, 47.7 % and 660 J m-2h-1, respectively) at different substrate (acetate) feedings (2.15 - 8.6 mM). System performance was characterized in the light of oxygen and acetate crossovers. The effect of membranes (in relation to the oxygen mass transfer coefficient, kO) on the microbial diversity of anodic and membrane-surface biofilms was investigated. Based on the relative abundance of bacterial orders, the two populations could be distinguished and membranes with larger kO tended to promote more the air-tolerant microbes in the biofouling layer. This indicates that membrane kO has a direct effect on membrane foulant microbial composition, and thus, on the expected time-stability of the membrane.