The contamination of agricultural land with heavy metals is a global concern. Agricultural products produced in heavy metal-contaminated soil are prone to metal accumulation, and thus, are less fitted for consumption due to food safety issues. The cultivation of biofuel crops in contaminated soil would provide immediate economic benefit to the landholders while simultaneously reclaiming contaminated sites in the long run. The use of edible soybean for biodiesel production is discouraged due to the negative impact on food security. However, soybean produced in metal-contaminated soil would be suitable for biodiesel production. In this study, the tolerance and metal bioaccumulation potential of Pseudomonas putida KNP9 for Pb and Cd is investigated, and KNP9 is tested for soybean growth enhancement in cadmium and lead-amended soil. The maximum metal tolerance for the Pb and Cd in KNP9 was 1580 µM and 546 µM, respectively. KNP9 was found to be effective in removing both Pb and Cd from the solution. SEM-EDX revealed that KNP9 bioaccumulates both Pb and Cd. In pot trial studies, KNP9 was found to be effective in enhancing soybean growth with respect to untreated control under lead and cadmium stress. Thus, KNP9 inoculation protects soybean plants from the detrimental effects of cadmium and lead stress. Therefore, metal bioaccumulating bacterium P. putida KNP9 inoculation in soybean is a promising strategy for soybean growth enhancement, which could be utilized for enhanced biodiesel production from soybean at metal-contaminated sites.