Soil genesis is a dynamic and complex geo-ecological process. Weathering of the parent material depends on physical chemical and biological factors and their interlinking however biological role in weathering is not yet fully established.In the present investigation microbial activity, diversity, physiology and mechanisms underlying in the weathering of miliolitic limestone were elucidated by undertaking integrative approach. Staphylococcus sp., Bacillus sp. and Actinomycetes sp. were abundantly distributed in miliolite. The principle mechanism involving in bacterial mediated miliolite dissolution was found to be organic acid production. Calcite dissolution was confirmed by XRD pattern. In situ microcosm experiments revealed the bacterial activity in dissolution of calcite. Erosion of miliolite was well documented by SEM. Results obtained from bacterial physiology indicated that these bacterial species were able to get nutrients form miliolite as a result miliolite weathering occurs.