•The production of bioenergy from waste is an essential component in the global development of sustainable energy sources. Anaerobic digestion (AD), which is the most prominent bioprocess technology for waste valorisation worldwide, uses undefined microbial cultures to produce energy rich compounds, such as alcohols, volatile fatty acids and biogas from organic substrates. However, poor operational stability still prevents AD from being widely commercialized. A wide variety of inhibitory substances, which can either be substantially present in wastes, or released during their degradation can induce anaerobic digester upset or failure. Among them, phenolic compounds are well-known inhibitors of the degradation of organic matter, halting the degradation process and biogas production. •Different authors suggest that besides technological improvements of the processes such as reactor design, AD efficiency could be further optimized by engineering and shaping its microbiota with external environmental levers, such as operating parameters, toward the desired functioning (Carballa et al. 2015). In particular, to confront future disturbances, the best strategy could consist in provoking a previous adaptation of the microbial communities to stressful conditions (McMahon et al. 2004). Pulse-feeding promotes for example higher capacity to confront perturbations (De Vrieze et al. 2013). •In this framework, we evaluated the possibility to increase the resistance of an anaerobic microbiota to phenol through an acclimatization strategy. To this end, different disturbance episodes of increasing importance were applied in a laboratory semi-continuous anaerobic bioreactor. Modifications of the anaerobic microbiota and of its performances were comprehensively analysed during extended reactor operation.