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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 nosZII gene. The trade-off effect of bio-organic substitution on N 2 O emissions may be due to the stimulated activity of the AOA-amoA 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 nosZII gene abundance. These findings suggest that conventional or bio-organic substitution is a promising strategy for alleviating the environmental costs of crop production., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)