Since urease-based microbial induced calcium carbonate precipitation (MICCP) process produces high ammonia levels, alternative strategies are very useful in adopting the MICCP process for bioremediating heavy metals. This study aimed to investigate the potential application of two native L-asparaginase and urease-producing isolates and Sporosarcina pasteurii as an indicator strain in removing zinc (Zn) from a contaminated solution and immobilizing it in soil through MICCP method. Zn removal from contaminated solution was 70.36% and 71.46% in 4 mmol L−1 Zn by S. pasteurii and urease-producing isolate, respectively. However, it was 97.32% when L-asparaginase-producing isolate was inoculated in solution with doubled Zn concentration (8 mmol L−1 Zn). The overall mean reduction of Zn in soluble-exchangeable fraction of soil was the highest in L-asparaginase-producing isolate treatment (71.8%) in comparison to S. pasteurii (61.8%) and urease-producing isolate treatments (56.2%). In contaminated soil with 150, 300, 400, and 500 mg kg−1 Zn, carbonate-bound Zn fraction increased to 79.2–85.35% and 83.86–85.12% in soil inoculated with S. pasteurii and urease-producing isolate, respectively. However, this fraction increased to 80.67, 84.95, 85.45, and 86.05%, respectively, in the case of L-asparaginase-producing isolate inoculation. Overall, the results confirmed the efficacy of both isolated strains in removing and immobilizing Zn in comparison to the indicator strain, which indicated the higher potential of the L-asparaginase strain. Therefore, due to the less ammonia production, L-asparaginase based MICCP process can be considered as a more environmentally friendly approach for bioremediating soil heavy metal.