Three baseline periods were established, corresponding to the three periods before each of the applied shocks. The performance of the intermittent systems operating under baseline conditions was better than the observed for the continuous systems concerning methanisation efficiency, in agreement with other reports [47], [52] and [53]. Under baseline conditions, the average values of this parameter ranged 86%–90% and 53%–58%, for the intermittent and the continuous systems, respectively. The average COD removal efficiencies in baseline operation ranged 94%–96% for the intermittent systems, and 85%–90% for the continuous systems. These differences in operational results have been attributed to the feedless phase of intermittent operation [54], in which the anaerobic biomass is forced to adapt to complex substrates difficult to degrade (mainly fats and LCFA), by means of microbial population shifts that raise the relative abundance of the Syntrophomonadaceae group [47] involved in the degradation of fatty substrates. In fact, the relative abundance of the Syntrophomonadaceae group in the microbial population developed in the intermittent systems operating at baseline conditions ranged from 17% to 20%, while this key microbial group was not present at detectable levels in the continuous systems throughout all the experiments performed in this work.