Abstract Ubiquitous bio-minerals exert significant effects on the migration and transformation of metal ions in the environment, however, research into the adsorption of heavy metals by biogenic vaterite (BV) has rarely been reported. The aim of our research was to evaluate the removal effects of Cd2+, Ni2+, and Cu2+ in single and multi-metal ion aqueous solutions using BV induced by Bacillus subtilis. The results demonstrate that the adsorption data of BV for metal ions are more accurately fitted to the Langmuir model compared with the Freundlich model. The max adsorption capacity (mg/g) order of BV was Ni (270.27) > Cu (178.57) > Cd (172.41) in a single-metal system, and Cu (175.44) > Ni (94.34) > Cd (30.30) in a multi-metal system (pH = 5.0, 2.5 g/L). A competitive effect exists amongst heavy metals in multi-metal ion systems, and Cu2+ adsorption is less affected by other two ions. Furthermore, BV can maintain favourable adsorption characteristics even in a very strong acidic environment (pH = 3.0), and its adsorptive capability becomes more favourable at higher temperatures. Kinetic analysis shows that the adsorption process can be better described by a pseudo-second-order model. XRD, FTIR, and SEM-EDS results reveal that metal ion adsorption on BV mostly happened through physical means, and the favourable adsorption characteristics of BV might be attributable to its larger specific surface area, aggregated spherical polyporous and organic–inorganic structure. Graphical abstract Unlabelled Image Highlights • Adsorption of single and multiple-metals on biogenic vaterite was investigated. • A Langmuir model describes metal ion adsorption by biogenic vaterite. • Biogenic vaterite is effective for Cd2+, Ni2+, and Cu2+ adsorption at pH ≥ 3. • Biogenic vaterite can be regarded as an organic-inorganic composite. [ABSTRACT FROM AUTHOR]