Soil management using fertilizers can modify soil chemical, biochemical and biological properties, including the concentration of trace-elements as cadmium (Cd), chromium (Cd) and nickel (Ni). Bacterial isolates from Cd, Cr, and Ni-contaminated soil were evaluated for some characteristics for their use in bioremediation. Isolates (592) were obtained from soil samples (19) of three areas used in three maize cultivation systems: no-tillage and conventional tillage with the application of mineral fertilizers; minimum tillage with the application of sewage sludge. Four isolates were resistant to Cr3+ (3.06 mmol dm−3) and Cd2+ (2.92 mmol dm−3). One isolate was resistant to the three metals at 0.95 mmol dm−3. All isolates developed in a medium of Cd2+, Cr3+ and Ni2+ at 0.5 mmol dm−3, and removed Cd2+ (17–33%) and Cr6+ (60–70%). They were identified by sequencing of the gene 16S rRNA, as bacteria of the genera Paenibacillus, Burkholderia, Ensifer, and two Cupriavidus. One of the Cupriavidus isolate was able to remove 60% of Cr6+ from the culture medium and showed high indole acetic acid production capacity. We evaluated it in a microbe-plant system that could potentially be deployed in bioremediation by removing toxic metals from contaminated soil. Display omitted •Bacterial isolates (592) were obtained from Cd, Cr, and Ni contaminated soil.•Several isolates showed resistance to more than 2 mmol dm−3 of Cd2+, Cr3+, and Ni2+.•One isolate was simultaneously resistant to about 1 mmol dm−3 Cd2+, Cr3+, and Ni2+.•Cupriavidus sp. removed 60% of Cr6+ from the culture medium.•Cupriavidus sp. produces IAA in the culture medium and showed potential for use in bioremediation.