The purpose of the present study is to synthesise quaternized poly (ether imide) (QPEI) membrane and its utilization as an anion exchange membrane (AEM) for microbial fuel cell (MFC) applications. The membrane's structural characterizations were confirmed by FT-IR and H-1 NMR spectroscopy. The surface morphology was obtained by SEM and the surface roughness was determined using non-contact profilometer. The effect of surface roughness, water uptake on anti biofouling properties were studied. The influence of oxygen and specific substrate crossover on the anode and cathode potential were also discussed. The performance stability of a single chambered MFC (SCMFC) was compared with that of dual chambered MFC (DCMFC). The investigations on QPEI and the commercially available AEM (AMI-7001) revealed that the QPEI membrane showed good static and kinetic properties over the AEM-7001 membrane. An enhanced water uptake percentage and reduced membrane surface roughness were bound to improve the overall MFC performance. (C) 2016 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.