The remediation of heavy metal contaminated sites using microbially induced carbonate precipitation is a promising technology. However, the carbonate, various minerals, and pH of the topsoil-rich surrounding environment strongly influence the heavy metal fugacity pattern during biomineralization in contaminated sites in Northwest China. The intrinsic influencing mechanism requires further investigation. In present study, contaminated loess specimens underwent one-dimensional soil column experiments with varying Cu(II) concentrations (500 mg/kg, 2 000 mg/kg, and 4 000 mg/kg). Subsequently, they were remediated by injecting different volumes (50 mL and 100 mL) of bacterial colloid. The remediation efficiency of soil samples at different depths was analyzed using Tessier sequential extraction, soil pH measurements, and X-ray diffraction (XRD). The results indicated that injecting bacterial cements converted exchangeable Cu into a less biotoxic form (e.g., carbonate-bound Cu). However, no similar transformation of Cu was observed at lower Cu(II) levels (500 mg/kg). The transformation of Cu forms in soil samples at various depths of the soil column correlated strongly with the pH of the surrounding environment. The pH, in turn, was positively associated with the volume of the injected bacterial colloid. The alkaline environment further enhanced the coordination adsorption of Cu and minerals in the loess. Nevertheless, with further alkalization, the remediation efficiency decreased significantly due to the formation of Cu-ammonia complexes. These results underscore the potential of utilizing microbially induced carbonate precipitation (MICP) technology for remediating Cu-contaminated sites.