The urease-based microbially induced carbonate precipitation (MICP) is known as effective remediation strategy in soil metals remediation; however, all related studies confined to bioaugmentation. In the present study, biostimulation process was adopted for the first time in accelerating MICP in copper (Cu) immobilization in soil. The abundance, composition, and diversity of the bacterial community after biostimulation were assessed with MiSeq Illumina sequencing analysis that confirmed number and types of ureolytic and calcifying bacteria grown significantly leading to MICP process, compared to untreated soil. The results demonstrated that biostimulation induced calcite precipitation in soil that immobilized Cu mainly in carbonated fraction of soil, while soluble-exchangeable fraction decreased from 45.54 mg kg−1 to 1.55 mg kg−1 Cu in soil. Scanning electron microscopy (SEM) cum energy-dispersive X-ray spectroscopy (EDX) evaluated structure and elemental composition in Cu immobilization after biostimulation. Fourier Transform-Infra Red (FTIR) spectroscopy depicted functional chemical groups involved in copper immobilization, while X-Ray Diffraction (XRD) identified main crystalline phases or biominerals formed during biostimulation in order to carryout Cu remediation from soil.