BackgroundUnderstanding the functional diversity, composition, and dynamics of microbiome is critical for quality in composting. Denitrifying microbiota, possessing multiple metabolic pathways simultaneously. Denitrification-based biodegradation of aromatic metabolites has been widely applied in the bioremediation of sediments. However, role in biodegradation of denitrifying microbiota in kitchen waste composting remain unclear. In this study, microbiome and metabolome were used to comprehensively decipher the relationship of denitrifying microbiota and aromatic metabolites, and its implication in kitchen waste (KW) composting.ResultsThis study was investigated by adjusting moisture content 60% as control test (CK), 70% as denitrification test (DE). In addition, one tests referred as DE + C, which received 10% of biochar to amend denitrification. Results indicated the quantities of denitrification genesnarGwere 1.22 × 108copies/g in DE at the 55th day, which were significantly higher than that in CK and DE + C (P< 0.05). Similarly, the abundance ofnirKgene also significantly increased in DE (P< 0.05). The relative abundance of denitrification-related microbes in DE was higher than that in CK, DE + C could weaken their abundance. Metabolomics results demonstrated that metabolites were downgraded in aromatic amino acid and catechin metabolic pathways in DE, which were identified as precursors to synthesis key product fulvic acid. The concentrations of fulvic acid dramatically decreased 21.05 mg/g in DE comparison with CK. Biochar addition alleviated the biodegradation of aromatic metabolites and reduced the utilization of fulvic acid. Integrative analyses of metabolomics and microbiome suggested that the microbiota involved in nitrite reduction pathway was vital for the biodegradation aromatic metabolites. Mantel test verified that NO3--N, moisture content, eta, environmental factors were important drivers behind the changes in the denitrifying microbiota biodegradation function.ConclusionThe data confirm the biodegradation function of denitrifying microbiota led to the loss of core product fulvic acid in KW composting, which highlighted the adverse role and implication of denitrification for composting humification. Control of denitrification with biochar was recommended to improve composting quality.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40793-023-00496-8.