Background and aim <p>Rice paddy soils represent a significant source of global methane emissions. In recent years, various soil amendments have been found to have the potential to reduce methane emissions. The effects and mechanisms of stevia residue on carbon sequestration and methane emissions in paddy soils remain unclear.</p> Method <p>A pot experiment used biochar (BC) as a positive control to assess the effect of stevia residue (VK) on methane emissions from paddy soil. We then measured changes in soil properties, physical fractions of soil organic carbon and soil aggregate stability indices, methane-cycling microbial community compositions, and CH₄ emissions, and thus the mechanisms through which stevia residue influences methane emissions from rice paddy soil were revealed.</p> Results <p>VK and BC significantly improved soil aggregate stability and organic carbon fraction stability, thereby reducing methane emissions from paddy soils. VK further influenced the microbial environment by increasing available nutrients and belowground biomass while lowering soil pH. Both treatments enhanced the abundance of methanotrophs and suppressed methanogens, with distinct shifts in microbial community composition.</p> Conclusions <p>This study demonstrates that stevia residue functions as a dual-purpose amendment, simultaneously reducing CH₄ emissions from paddy soils and enhancing carbon sequestration. It provides a sustainable strategy to integrate soil fertility improvement with greenhouse gas mitigation in intensive rice agriculture.</p> Graphical Abstract <p></p>