Background and Aims <p>Cadmium (Cd) and arsenic (As) co-contamination in paddy soils poses serious risks to both rice safety and human health. Although manganese (Mn) and selenium (Se) have been individually reported to mitigate Cd or As accumulation in plants, their combined effects on Cd-As co-contaminated systems remain poorly understood, particularly through mineral-element migration-microbial co-regulation.</p> Methods <p>A pot experiment was conducted to investigate the effects of Mn and Se on Cd and As accumulation in rice. A newly introduced parameter, the mineral element diffusion index (DI), was applied to quantify the gradient distribution of these elements in the rhizosphere or bulk soil. Furthermore, the relationship between DI and the soil microbial symbiotic network was analyzed to explore their combined influence on the regulation of Cd and As accumulation in rice.</p> Results <p>Mn-Se co-application synergistically reduces Cd (40.12%) and As (83.80%) concentration in brown rice, significantly outperforming single-element treatments. Key mechanistic insights reveal that Mn-Se co-application: (i) Reshapes rhizosphere and bulk soil microbial co-occurrence networks, specifically enriching and activating functional rhizosphere communities; (ii) Enhance essential mineral elements gradients toward the rhizosphere, creating a biogeochemical barrier that impedes Cd and As translocation; (iii) Stabilizes functional microbial modules centered on the S and Ti element diffusion index, reducing soil bioavailable Cd and As concentrations.</p> Conclusion <p>Mn-Se co-application reduces Cd and As accumulation in rice by reshaping the rhizosphere microbiome and sharpening elemental gradients at the soil interface. These results offer new insights into the biogeochemistry of Cd or As immobilization and support the development of targeted rhizosphere management strategies for Cd-As co-contaminated paddies.</p> Graphical Abstract <p></p>