Microbially induced carbonate precipitation (MICP) driven by Sporosarcina pasteurii was highly efficient for heavy metal (i.e., Cd²⁺, Cu²⁺ and Pb²⁺) removal in the range of 50 to 800 mg/L. Sporosarcina pasteurii bacteria were sequentially inoculated in nutrient broths amended with increased concentrations of heavy metals separately to improve the resistance to heavy metal environments. In the absence of Ca²⁺, the increasing urea concentration was conducive to Cd²⁺ removal with the best removal ratio 89.9–99.7% at a urea concentration of 2.0 mol/L, but had little positive effect on Cu²⁺ and Pb²⁺ removal, with a removal ratio of 62.6–64.4% and 71.4–97.6%, respectively, at a urea concentration of 0.5 mol/L. The heavy metal coprecipitated with Ca²⁺, leading to much more effective heavy metal removal, and the removal efficiency of Cd²⁺, Cu²⁺ and Pb²⁺ could reach 98.0–99.0, 78.1–82.1 and 98.0–100.0%, respectively. The Cu²⁺ deposit aggregated and cemented to form clusters, different from Cd²⁺ and Pb²⁺ deposits with comparatively dispersed microstructure. For all the three heavy metal precipitates, the predominant mineral was identified as calcite, the most thermodynamically stable polymorph of CaCO₃.