First large-scale experiences of bioelectrochemical systems (BES) are underway. However, there is still little knowledge on how the different elements that integrate a BES behave in near real-life conditions. This paper aims at assessing the impact of long-term operation on the cation exchange membrane and on the anodic biofilm of two 16 L Microbial Electrolysis Cells (MEC) designed for hydrogen production and ammonia recovery from pig slurry. Membrane deterioration was examined by physical, chemical and microscopy techniques at different locations, revealing a strong attachment of microorganisms and a significant decay in membrane properties such as ion exchange capacity and thermal stability. Anode microbial communities did not show a dramatic shift in the eubacteria composition at different sampling areas, although the relative abundance of some bacterial groups showed a clear vertical stratification. After 100 days of continuous operation, MEC performance did not declined significantly maintaining ammonium transport rates and H-2 production rates of 15.3 gN d(-1) m(-2) and 0.2 LH2 center dot L-1 (reactor)center dot d(-1) respectively. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.