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Previous studies reported a reduction in N2O emissions following lime application. However, the mechanisms underlying N2O reduction under different soil acidifications are not clear and require further investigation. As a result, it is imperative to gain insights into how lime application affects N2O emissions and associated microbial activities under varying soil acidification and other factors. Only studies obtained from the agroecosystems were considered for the current meta-analysis. Accordingly, this meta-analysis was conducted with 684, 141, 149, and 94 paired observations for the response variables of N2O emissions, archaeal amoA gene abundance, bacterial amoA gene abundance, and nosZ gene abundance, respectively, obtained from 39 peer-reviewed studies. The current meta-analysis findings indicated that the lime application reduced soil N2O emissions by 46.63 % and raised soil pH by 27.63 % across all paired observations compared to control. Overall, lime application also increased the abundance of bacterial amoA and nosZ genes by 101.17 % and 49.63 %, respectively, while decreasing the abundance of archaeal amoA by 6.39 %. Our structural equation modeling (SEM) suggested that the differences in the reduction of N2O emission magnitudes under different lime rates are due to differences in the degree of soil pH manipulation. Lime application rate was identified as the primary factor influencing the response of soil N2O emissions to lime, followed by soil pH. Our results from SEM indicated that the main drivers of the variable responses in soil N2O emissions to lime application under different soil acidifications are the variable responses of N2O-associated microbial activities and substrate availability. The greater reduction in N2O emissions under neutral soil conditions, compared to acidic conditions, is primarily attributed to a pH-driven shift in microbial activity, evidenced by a larger increase in nosZ gene abundance and a decrease in bacterial amoA gene abundance. Grain yields of wheat, rice, and maize increased by 9.42 %, 11.40 %, and 62.42 %, respectively, following lime application compared to the control. Based on our findings, we concluded that applying lime to acidic soils is a suitable option for reducing soil N2O emissions by affecting the activity of associated microbial functional genes and substrate availability in agricultural ecosystems.