•Within digesters, anaerobic microorganisms responsible for biological conversion of organic material into methane (CH4) are vulnerable to a wide variety of inhibitory substances or factors which result in decreased production yields (Chen et al., 2008). Among them, ammonia is regularly mentioned as the primary cause of digester failure (Rajagopal et al., 2013). This compound can be found at high concentration in many traditional AD substrates such as livestock manure, slaughterhouse by-products and food industrial residues due to the presence of organic nitrogen such as urea and proteins which readily release ammonia upon digesters during their degradation (Yenigün & Demirel, 2013). •In order to get more insights into biological mechanisms governing complex ecosystems facing inhibitions, this study aims at examining microbial structural changes caused by ammonia. A better understanding of microbial community response to different levels of perturbation could enable to identify key phylotypes potentially involved in AD microbiota resistance. The possibility of identifying early warning microbial indicators correlated with the decrease of AD performance was also questioned.