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Winery effluents are agro-industrial wastes that can be treated to produce methane in anaerobic digestion systems. Understanding how the process configuration and operating conditions affect the microbial communities and their metabolism is essential to improve the performance of these systems. This work aimed to compare the taxonomic and functional profiles of four process configurations of an anaerobic digestion system treating winery effluents. Taxonomic profiles were obtained by sequencing the 16S rRNA gene, and the Tax4Fun2 package was used to predict the functional profiles. Different genera predominated under three configurations in the acidogenic reactor, Sporolactobacillus, Prevotella and Acetobacter, respectively; however, the analysis indicated high functional redundancy among configurations. Methane production by the acetoclastic pathway was mainly related to Methanosaeta in the single-stage configuration and related to five different archaea genera in the two-stage configuration. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis predominated under thermophilic conditions, where Methanothermobacter had up to 65% of the relative abundance. The two-stage configuration was more stable due to the higher microbial diversity and functional redundancy than the single-stage; the microbial community in mesophilic conditions also had higher microbial diversity and functional redundancy than in thermophilic conditions; finally, applying harsher operating conditions reduces the microbial diversity and the stability of the process. This analysis provided valuable knowledge to understand and improve methane production in anaerobic digestion systems.