Purpose <p>To determine the optimal agricultural management practices for mitigating soil greenhouse gas emissions, in this study, the effects of straw incorporation and nitrification inhibitors (NIs) on soil greenhouse gas emissions and bacterial communities in fluvo-aquic soil were evaluated.</p> Methods <p>Straw and NIs, nitrapyrin (CP) and dicyandiamide (DCD), were applied either individually or in combination. The treatments were as follows: urea alone (SU), urea + CP (CP), urea + DCD (DCD), urea + straw (S), S + CP (SCP), and S + DCD (SDCD).</p> Results <p>Compared with those in the SU treatment, the cumulative N₂O emissions in the DCD treatment increased by 30.6%, but the difference was not significant (<i>p</i> &gt; 0.05). Straw application significantly increased cumulative N₂O emissions (<i>p</i> &lt; 0.05). Compared with the S treatment, the SCP and SDCD treatments significantly decreased cumulative N₂O emissions by 79.8% and 53.7%, respectively. Additionally, DCD significantly decreased soil CO₂ emissions under straw incorporation. At the phylum level, the relative abundances of Proteobacteria, Bacteroidota and Firmicutes increased following straw amendment. A significant increase in the abundance of Proteobacteria was observed in the SDCD treatment, whereas increases in the abundances of Bacteroidota and Patescibacteria were noted in the SCP treatment. Stepwise linear regression analysis revealed that the relative abundances of Firmicutes and Bacteroidota significantly affected soil CO₂ flux.</p> Conclusions <p>Our findings indicate that appropriate selection of NIs is essential for mitigating greenhouse gas emissions. The long-term use of NIs requires further evaluation to ensure the sustainability of agricultural ecosystems.</p>