Anaerobic digestion is an environmental key technology in the future bio-based economy. To achieve functional stability, a minimal microbial community diversity is required. This microbial community should also have a certain ‘elasticity’, i.e. the ability to rapidly adapt to suboptimal conditions or stress. In this study it was evaluated whether a higher degree of functional stability could be achieved by changing the feeding pattern, which can change the evenness, dynamics and richness of the bacterial community. The first reactor (CSTRstable) was fed on daily basis, whereas the second reactor (CSTRdynamic) was fed every 2 days. Average biogas production was 0.30 l CH4 l−1 day−1 in both reactors, although daily variation was up to four times higher in the CSTRdynamic compared with the CSTRstable during the first 50 days. Bacterial analysis revealed that this CSTRdynamic had a two times higher degree of bacterial community dynamics. The CSTRdynamic also appeared to be more tolerant to an organic shock load of 8 g COD l−1 and ammonium levels up to 8000 mg TAN l−1. These results suggest that the regular application of a limited pulse of organic material and/or a variation in the substrate composition might promote higher functional stability in anaerobic digestion.