Purpose Agricultural soil contamination by heavy metals is a serious environmental problem, and developing feasible and effective soil remediation technologies is a top priority. In this study, a microbial consortium dominated by sulfur-oxidizing bacteria was constructed to enhance Cd and Zn removal from contaminated soil. Materials and methods During treatments, changes in pH and Eh and the removal efficiencies of Cd and Zn were investigated. Fractionation of Cd and Zn, soil fertility indexes, and the microbial community were also analyzed before and after bioleaching. Results and discussion The results show that under the same conditions, the best removal efficiencies for Cd and Zn were observed in the bioleaching group compared to other treatments (acid leaching and sulfur treatment). When the sulfur concentration was 15 g/kg, 79.3% of Cd and 45.2% of Zn were removed, while undissolved Cd and Zn mainly remained in the residual fraction, accounting for 93.1% and 84.0% of their remaining totals, respectively. After remediation, the bioleaching group showed a reduction of the total phosphorus and available potassium, with a decrease of 53.7% and 41.2%, respectively. Furthermore, the exogenous microbes in the inoculum had a competitive advantage and became the dominant population at the end of the run. Conclusions The consortium obtained in this study can effectively improve remediation processing and be used to remediate heavy metal-contaminated soil.