Mineralogically distinct coal samples respond differently to microbial attack. In the present study, a mixed meso-acidophilic bacterial consortium predominantly comprising ofAcidithiobacillus ferrooxidansstrain was investigated for its biodesulphurization abilities for three distinct sulphur bearing samples (Goa CPC, Rajasthan Lignite, Assam Coal) of Indian origin in iron (9K(+)) and iron-free (9K(-)) media. A media devoid of Fe (II) iron was more effective for sulphur removal with maximum desulphurization of 45.19% for Assam coal followed by 36.8% for Rajasthan Lignite and 23.38% for CPC respectively. The proximate analysis, FTIR patterns and XRD analysis of the samples provided better insights into understanding the mineralogical and compositional changes in the coal matrix. Owing to the higher efficiency, Assam coal was additionally subjected to further optimization studies and characterization of the treated coal through TGA. The study indicated that the gross calorific values for all the samples increased following microbial treatment in 9K(-)media thereby providing a scope for further scale-up studies.