Nanocomposite membranes are a promising alternative for proton exchange membrane (PEM) because it has the capability of transferring protons, is inexpensive, and also have higher resistance against fouling compared to other membranes in microbial fuel cells (MFCs). In this study, Saccharomyces cerevisiae was used as an active biocatalyst and neutral red with low concentration (200 mu mol I-1) was selected as electron shuttle in anode chamber. Moreover, four different concentrations of Fe3O4/PES have been tested as new generation of nanocomposite membrane and its efficiencies were compared with Nafion 117 in dual chamber MFC. To improve the performance of PEM, several nanoparticle (5%, 10%, 15% and 20% of Fe3O4 nanoparticle) concentrations were used. Maximum generated power and current with new synthesized membrane and 15% Fe3O4 nanoparticle were 20 mW m(-2) and 148 mA m(-2), while it was 15.4 mW m(-2) and 112 mA m(-2), respectively by using Nafion 117 at the same experimental condition. The highest obtained voltage was 656 mV and it was stable for 72 h of operation time. (C) 2011 Elsevier Ltd. All rights reserved.