Aims <p>Nitrous oxide (N₂O) from agricultural soils is a potent greenhouse gas and a dominant ozone-depleting substance, underscoring an urgent need for sustainable mitigation strategies. Plant growth-promoting rhizobacteria (PGPR) represent a promising bio-based solution, given their dual role in enhancing plant productivity and regulating soil N cycles.</p> Methods <p>This study investigates the mechanisms by which PGPR regulate N₂O emissions in two contrasting soils (paddy-upland rotation and upland-upland rotation). PGPR inoculation treatments were applied to examine their effects on N₂O fluxes. Quantitative real-time PCR (qPCR) was used to measure nitrogen-cycling gene abundances, and high-throughput sequencing analyzed soil microbial community composition. Correlation analysis, Mantel tests, and Random Forest modeling identified core microbial taxa influencing N₂O fluxes.</p> Results <p>PGPR efficacy was found to be co-determined by native soil properties and strain functional traits. In Wuxi soil, effective PGPR strains suppressed nitrification gene abundance (<i>AOA-amoA</i>, <i>AOB-amoA</i>) while enriching key denitrifiers such as <i>Rhodanobacter</i>, thereby constraining N₂O production and enhancing its reduction. In contrast, in Dezhou soil with upland-upland rotation, successful mitigation involved optimizing the microbial consortium to favor a synergy between low-N₂O-yield ammonia oxidizers (e.g., <i>Nitrososphaeraceae</i>) and efficient denitrifiers. Furthermore, we identified and validated key microbial taxa (e.g., <i>Lysobacter</i> and <i>Vicinamibacteraceae</i>) whose abundances strongly correlated with N₂O flux. These findings provide a mechanistic framework for tailoring PGPR inoculants to specific soil environments, advancing their application as a precise and sustainable tool for mitigating agricultural N₂O emissions.</p> Conclusions <p>The <i>nosZ</i>-carrying strain YSQ030 exhibited stable N₂O mitigation performance in both Wuxi and Dezhou soils.</p> Graphical Abstract <p></p>