This study developed a novel calcium-based magnetic biochar by pyrolysing rice straw mixed with calcium carbonate and iron oxide for stabilization of contamination of multiple metals. A 160-day incubation study was conducted to investigate its performance in stabilization of cadmium and arsenic co-contamination in soil. Both biochar and Ca-MBC treatments increased soil pH, decreased the bioavailability of cadmium. Ca-MBC decreased but biochar enhanced the bioavailability of arsenic. The BCR (European Community Bureau of Reference) sequential extraction confirmed Ca-MBC facilitated the transformation of the unstable fraction of arsenic to stable fractions. The stabilization mechanisms were explored through synchrotron-based micro X-ray fluorescence and X-ray absorption near edge structure. The results show that Ca-MBC remediated the dual contamination of arsenic and cadmium through (1) elevated pH and cation exchange capacity (for Cd); (2) the formation of bi-dentate chelate and ternary surface complexes on the surface of iron oxide; (3) enhanced adsorption ability of porous biochar. In addition, Ca-MBC increased the abundance and diversity of bacterial community, and modified the relative abundances of bacterial taxa, leading to a shift of the composition. These new insights provide valuable information for stabilization of co-contamination of arsenic and cadmium in soil using the potential material Ca-MBC.