• Ureolytic microbes affect the surface structure of phosphate minerals by CO 3 2− release. • Concave increases the surface area of PR and exposes more active adsorption sites. • FPR for Cd 2+ adsorption is a spontaneous endothermic monolayer fast process. • Enhanced complexation and ion exchange dominate the adsorption mechanism. • A green approach to developing cost-effective mineral for Cd remediation is provided. Heavy metal pollution restricts the intensification of land and endangers human health through the food chain. Surface adsorption of heavy metals by soil natural minerals affects their mobility and biotoxicity, yet little is known about the fate of heavy metals after microorganisms affect the surface structure of minerals. Our study shows that ureolytic microbes corrode the surface of phosphate minerals through carbonate modification without changing their crystal structure but significantly enhancing their specific surface area. Compared with natural phosphate rock (PR), the concave surface of the flora-phosphate rock (FPR) exposes more Ca 2+ exchange sites, more active functional groups, and more straightforward to release phosphates that co-precipitate with Cd 2+ , resulting in an approximately tenfold increase in Cd 2+ adsorption. The adsorption of Cd 2+ by FPR is a spontaneous endothermic single-layer adsorption, which can quickly remove Cd 2+ in wastewater. FPR can also obviously change the pH of the soil by releasing phosphate to increase the stabilization effect of Cd 2+ . These results provide a sustainable approach to developing novel, cost-effective minerals for environmental remediation and contribute to understanding the function and role of microorganisms in immobilizing heavy metals at the mineral interface.