•Isolation of Bacillus aryabhattai-related bacterial isolates with zinc-solubilizing abilities.•Bacterial isolates produced organic acids and solubilized insoluble zinc compounds.•Rhizosphere inoculation of two crops mobilized native soil zinc from unavailable forms.•Improved growth, yield and zinc content in soybean and wheat crops upon inoculation.•First report of B. aryabhattai-related isolates from rhizosphere of soybean cultivated in India. Zinc deficiency not only affects crop yields, but also nutritional quality and human health. Microbial transformation of unavailable forms of soil zinc to plant available zinc is an important approach contributing to plant zinc nutrition and growth promotion. Therefore, the objectives were to (a) assess in vitro zinc solubilization ability of Bacillus aryabhattai strains MDSR7, MDSR11 and MDSR14 in medium supplemented with three insoluble zinc salts (zinc oxide, zinc carbonate and zinc phosphate) and (b) to evaluate their response of inoculation on crop growth, soil biological properties, zinc mobilization from native zinc-pool of soil and acquisition by soybean and wheat under microcosm conditions. The microcosm experiment comprised of five treatments for each crop, viz., (1) un-inoculated control without crop (non-rhizosphere soil); (2) un-inoculated control with crop; (3) B. aryabhattai MDSR7; (4) B. aryabhattai MDSR11; and (5) B. aryabhattai MDSR14 in completely randomized block design with twelve replications. While testing under in vitro, all the three strains possessed IAA, siderophore and ammonia producing traits. The strains MDSR7 and MDSR14 produced substantially higher soluble zinc content with significant decline in pH and increase in total organic acid production in Tris-minimal broth supplemented with insoluble zinc compounds. Further on inoculation with MDSR7 and MDSR14 substantially decreased rhizosphere soil pH and increased dehydrogenase, β-glucosidase, auxin production, microbial respiration and microbial biomass-C in the rhizosphere soils of soybean and wheat. The operation of all these soil processes regulated by B. aryabhattai strains resulted in a depletion of organically complexed and calcium carbonate bound zinc and an increase in exchangeable and sesquioxide bound zinc in soil. Such enhanced microbial activities and redistribution among different zinc pools in rhizosphere might have paved way for increased plant available zinc resulting in increased growth promotion and zinc assimilation in seeds by soybean and wheat crops. This assumes significance as the increased zinc concentration found in this study has large implications in terms of overcoming zinc malnutrition. We conclude that the strains MDSR7 and MDSR14 substantially influenced mobilization of zinc and its concentration in edible portion, yield of soybean and wheat, and can be utilized as bio-inoculants for biofertilization and biofortification.