Soil contamination by toxic heavy metals such as copper is a serious problem. In this study, the extracellular polymeric substance (EPS) extracted from Rahnella sp. LRP3 was found with the potential of immobilizing Cu-polluted in soil. The EPS could bond to Cu (II) through functional groups (polysaccharides, amide, proteins, and carboxyl groups), which further developed into the porous sphere with a diameter of 20 μm. Besides, EPS could induce the formation of Cu5(PO4)2(OH)4 crystal by the biomineralization process. Finally, the EPS in the culture solution reduced 89.4 mg/kg of DTPA-Cu content by 78.99% in soil for 10 d under the condition of 25 °C via biomineralization. The results demonstrated that EPS produced by Rahnella sp. LRP3 will be a promising factor in the remediation of Cu contaminated soil. Display omitted •The EPS extracted from Rahnella sp. LRP3 could remove Cu (II) in the solution through biosorption process.•The EPS further induced the formation of Cu-containing biomineral, identified as Cu5(PO4)2(OH)4.•The EPS decreased the content of available Cu in polluted soil via biomineralization process.