Anaerobic digestion (AD) has been commercially operated worldwide in full scale as a resource recovery technology underpinning a circular economy. However, problems such as a long start-up time, or system instability, have been reported in response to operational shocks. These issues are usually linked to the dynamics of the functional microbiota in AD. Exploring the microbiota-functionality nexus (MFN) could be pivotal to understand the reasons behind these difficulties, and hence improving AD performance. Here we present a systematic MFN study based on 138 samples taken from 20 well-profiled lab-scale AD reactors operated for up to two years. All the reactors were operated in the same lab within the same period of time using the same methodology to harvest physio-chemical and molecular data, including key monitoring parameters, qPCR, and 16S sequencing results. The results showed a core bacterial microbiota prevailing in all reactor types, including Bacillus, Clostridium, Bacteroides, Eubacterium, Cytophaga, Anaerophaga, and Syntrophomonas, while various methanogens dominated different communities due to different inocula origins, reactor temperatures, or salinity levels. This core bacterial microbiota well correlated with biogas production (Pearson correlation coefficient of 0.481, p < 0.0001). Such strong correlation was even comparable to that between the biogas production and the methanogenic 16S rRNA gene content (Pearson correlation coefficient of 0.481, p < 0.0001). The results indicated that AD performance only modestly correlated with microbial diversity, a key governing factor. AD microbiota was neither functionally redundant nor plastic, and a high variety in communities can exhibit a strong difference in reactor performance. Our study demonstrates the importance of a core bacterial microbiota in AD and supports inspiring considerations for design, bioaugmentation, and operational strategies of AD reactors in the future.