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To gain insight into the microbial mechanisms associated with the replacement of chemical fertilizers with organic or bio-organic fertilizers to mitigate soil nitrous oxide (N 2 O) emissions, we measured N 2 O emissions from greenhouse vegetable soils through field observations and pot experiments. Results showed that organic substitution suppressed N 2 O emissions by reducing soil mineral N content and stimulating the abundance of the nos ZII gene. The trade-off effect of bio-organic substitution on N 2 O emissions may be due to the stimulated activity of the AOA- amo A gene, resulting in unfavorable conditions for N 2 O production and thus reduced N 2 O loss. We also linked the inhibitory effect of organic and bio-organic substitution on N 2 O emissions to the increased abundance of key species in bacterial co-occurrence networks represented by Patescibacteria as they were significantly and negatively correlated with N 2 O emissions. However, the mitigation effect of bio-organic substitution on N 2 O emissions was conteracted by an increase in Bacillus abundance due to the direct negative effect of Bacillus on the nos ZII gene abundance. These findings suggest that conventional or bio-organic substitution is a promising strategy for alleviating the environmental costs of crop production. [Display omitted] • Organic substitution reduced both area-scaled N 2 O emission and vegetable yield. • Bio-organic substitution lowered yield-scaled N 2 O emission and boosted crop yield. • Keystone bacterial species played a crucial role in regulating N 2 O emission. • Bacillus inoculation raised N 2 O emission by reducing the abundance of the nosZII gene. [ABSTRACT FROM AUTHOR]