Display omitted •The bioaugmentation with Methanoculleus sp. culture remarkably enhanced the methane yield by 21%•The volatile fatty acids were decreased by 10% compared to the period before bioaugmentation.•Peptococcaceae and Tissierellales were dominating the microbiome as glucose degraders.•Syntrophaceticus was the key acetate oxidizer under the extremely high level of 13.5 NH4+-N/L.•Multiple glucose/acetate metabolism were reconstructed by metagenomic approach. The bioaugmentation is crucial to improve the energy-efficient process for anaerobic digestion of organic wastes at high ammonia levels. Genomic insights into the intricate microbial networks at a high ammonia level remain underexplored. The present study showed that the addition of Methanoculleus sp. DTU887 remarkably enhanced the methane production yield of organic fraction of municipal solid waste by 21% and decreased the volatile fatty acids by 10% when compared to the period before bioaugmentation. Genome-centric metagenomics reports the functional contribution of microbial members during organic waste degradation under the extremely high level of 13.5 g NH4+-N/L. Specifically, metabolic reconstruction revealed that these organisms have the potential to perform fermentative and acetogenic catabolism, a process facilitated by energy conservation-related with H2/CO2 metabolism. Peptococcaceae spp. (DTU903, DTU900, and DTU895). and Tissierellales sp. DTU879 could degrade the organic waste hydrolysis product, i.e., glucose to acetate and H2. Tissierellales sp. DTU879 and Syntrophaceticus sp. DTU783 could degrade the derived acetate. The H2 scavenging Methanoculleus sp. DTU887 performs complementary metabolic reactions with Peptococcaceae spp., Tissierellales sp. and Syntrophaceticus sp., indicating syntrophic glucose and acetate degradation. This research offers the first insight that the key organisms form a syntrophy-supported food web in response to the bioaugmentation with ammonia tolerant methanogens performed in an AD system subjected to severe ammonia inhibition.