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Overloading is one of the most typical process disturbance in anaerobic digesters, resulting in volatile fatty acids (VFAs) accumulation. This work aimed to study the microbial community dynamics during hydraulic (decreasing the hydraulic retention time (HRT)) and organic (increasing the organic loading rate maintaining the HRT constant) overload shocks in anaerobic reactors treating agro-industrial wastes, as well as during the recovery period. In both cases, the organic loading rate increased from 2 to 10 g COD L−1 d−1, resulting in VFAs accumulation up to 9 g L−1. Both overloads were correlated to an increase in Bacteroidetes and Actinobacteria phyla and with a drop in Syntrophomonadaceae and Pseudomonadaceae families. In contrast, Tissierellaceae family only increased during the organic shock. Active Archaea decreased in both overloads, going from Methanosaeta dominance to Methanosarcina prevalence. During the recovery period, Porphyromonadaceae family increased its presence and Clostridium genus recovered values prior to perturbation.