Bioelectrochemical systems (BES) encompass a group of bio-based technologies capable of directly converting organic matter into electricity. In these systems, which are derived from conventional electrochemical technologies, the ion exchange membrane is a key element because of its influence on the economic feasibility and performance of BES. This study examined the impact of the long-term operation of BES on the mechanical, chemical, and electrochemical properties of five different kinds of cation exchange membranes (Nafion-117, CMI-7000, Zirfon UTP 500, FKE, and FKB) through several techniques: (i) scanning electron microscopy and atomic force microscopy to assess the changes on the membrane surface, (ii) thermogravimetric analysis to evaluate the structural stability of the membranes, and (iii) ion exchange capacity to monitor any change in their electro-chemical properties. Results confirmed that there is not an ideal membrane for BES. While Nafion and CMI exhibited the strongest chemical structure, they also underwent the highest fouling, as revealed by a fast increase in surface roughness. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.