Worldwide overpopulation needs progressive crop yield creating environmental pollution. Low cost and easily available biofertilizer development is the best alternative for a sustainable agricultural system. In this study different agricultural waste such as wheat bran, sesame bran and bagasse were used as a carrier for the isolated PGPR. Two most potent cadmium and lead tolerant PGPR were isolated from Indian agricultural soil and identified as Lysinibacillus varians strain KUBM17 (accession number MG976681) and Pseudomonas putida strain KUBM18 (accession number MG976684). PGPRs were inoculated in different possible combinations of carrier materials. The growth and survivability of PGPRs were checked with plate count technique frequently up to 120 days. The best carrier was selected for PGPR application on radish and gram plants to check their plant growth-promoting ability. Sesame bran showed higher CFU count (7.8 x106/gm) for the PGPRs from the early days. Whereas, wheat bran and bagasse individually showed slower but sustainable nutrient availability for both the PGPRs. Wheat bran, sesame bran and bagasse in 1:1:1 ratio produced decent performance throughout the time period. The carrier mixture as biofertilizer showed higher plant biomass, germination percentage, chlorophyll content and other growth parameters on radish and gram plant under cadmium and lead stress. Carrier grown Lysinibacillus varians and Pseudomonas putida were able to nullify the toxicity of cadmium or lead and significantly (p < 0.05) enhanced almost all the plant growth parameters of both the plants. So, wheat bran, sesame bran and bagasse can be used for cheap PGPR-biofertilizer development.