The main objective of this study was to establish the metabolic pathway of a biogas fermentation system active at low temperature, and to describe the bacterial and archaeal methanogenic species responsible. A biogas fermentation inoculum adapted to be active at 9°C was used in a 10‐L batch‐type temperature‐controlled fermentor, using pig manure as the raw material. Fermentation at 9°C was followed for 120 days. A combination of nonbiological and biological factors was analyzed. Species were identified from OTU analysis based on 16S rDNA amplicon sequencing, and correlation analysis was used to study the effect of nonbiological factors, bacterial communities, and archaea communities. Biogas production was most effective between days 50 and 90, where gas production was above 0.70 L/d and the CH4 yield was above 0.36 L/g‐volatile solid. The relative abundance of the first dominant bacterial OTU with 99% identity to Clostridium cellulovorans varied between 16.17% and 27.30%. These bacteria typically degrade cellulose and hemicellulose. The second dominant bacterial OTU (relative abundance 15.23%‐27.15%) was 99% identical to Terrisporobacter petrolearius, a typical fermentative species. The most abundant (4.15%‐37.14%) archaeal OTU was 98% identical to Methanocorpusculum sinense, which is a typical hydrogenotrophic methanogen. A low‐temperature biogas metabolic pathway was constructed, based on abundant bacterial and methanogen OTUs. The most suitable metabolic pathway describes that hydrogen is produced by one part of the community and then used to reduce the produced carbon dioxide into CH4; this seems to be the major pathway by which biogas is produced under low‐temperature conditions.