Background and aims <p>Soil microbiome, influenced by plant activity, can affect the growth of subsequent plant species, a phenomenon known as plant-soil feedback. This feedback depends on the microbial legacies left by previous plants and fertilization practices. However, the impact of soil microbiome legacies induced by organic manure application on crop performance and greenhouse gas emission remains largely unknown. This study aimed to explore how fertilization regimes impact the composition and function of soil microbiome, as well as the associated microbial legacy effect on subsequent maize performance and greenhouse gas emissions.</p> Methods <p>In this study, we investigated bacterial, fungal, and protistan communities, as well as functional groups and gene abundances, under organic manure and chemical fertilizer applications in a 14-year field experiment. A pot experiment was conducted to explore the effects of microbial communities induced by these treatments on subsequent crop performance and greenhouse gas emissions.</p> Results <p>Organic manure application increased microbial alpha diversity while reducing plant pathogen abundance compared to chemical fertilizers. Improved crop performance under organic manure application was mainly attributed to increased microbial alpha diversity, rather than a reduction in plant pathogens. Organic manure enhanced the abundance of carbon degradation genes, leading to increased CO₂ emissions, but it reduced N₂O emissions via a reduction of nitrification and denitrification gene abundances compared to chemical fertilizers.</p> Conclusion <p>Our findings emphasize the legacy effects of soil microbiome under organic manure application are beneficial for improving crop performance and mitigating greenhouse gas emissions.</p>