Flooding of paddy fields enhances methane (CH4) emissions and arsenic (As) mobilisation, which are crucial issues for agricultural greenhouse gas emissions and food safety. Birnessite (δ-MnO2) is a common natural oxidant and scavenger for heavy metals. In this study, birnessite was applied to As-contaminated paddy soil. The capacity for simultaneously alleviating CH4 emissions and As mobility was explored. Soil microcosm incubation results indicated that birnessite addition simultaneously reduced CH4 emissions by 47 %–54 % and As release by 38 %–85 %. The addition of birnessite decreased the dissolved organic carbon (DOC) contents and altered its chemical properties. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) results showed that birnessite reduced the labile fractions of proteins, carbohydrates, lignins, tannins, and unsaturated hydrocarbons, however, increased the abundance of condensed aromatic structures, suggesting the polymerisation of dissolved organic matter (DOM) by birnessite. The degradation of labile fractions and the polymerisation of DOM resulted in an inventory of recalcitrant DOM, which is difficult for microbes to metabolise, thus inhibiting methanogenesis. In contrast, birnessite addition increased CH4 oxidation, as the particulate methane monooxygenase (pmoA) gene abundance increased by 30 %. The enhanced polymerisation of DOM by birnessite also increased As complexation with organics, leading to the transfer of As to the organic bound phase. In addition, the decrease in ferrous ion [Fe(II)] concentrations with birnessite indicated that the reductive dissolution of Fe oxides was suppressed, which limited the release of arsenite [As(III)] under reducing conditions. Furthermore, birnessite decreased As methylation and shaped the soil microbial community structure by enriching the metal-reducing bacterium Bacillus. Overall, our results provide a promising method to suppress greenhouse gas emissions and the risk of As contamination in paddy soils, although further studies are needed to verify its efficacy and effectiveness under field conditions.