The high sulfur content in North-East Indian coal is one of the primary challenges with using it as an energy source. Therefore, the present study uses Burkholderia sp. GR 8-02 to explore coal beneficiation from the Tipong mine (T20 and T60) in Assam (North-East India). Various particle size fractions (−125 to +210 µm, −210 to +250 µm, −250 to +297 µm, −297 to +400 µm and −400 to +500 µm) were treated and subjected to petrographic and chemical analysis, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS), Thermogravimetric analysis (TGA), and Raman spectral analysis. The results revealed a 39.04% and 32.43% reduction in total sulfur for T20 and T60 samples, respectively. The ash content decreased by 19.79% in the T20 coal sample and by 24.52% in the T60 coal samples, with a relative decrease in the mineral matter content of approximately 17.43%. Following beneficiation with Burkholderia sp. GR 8-02, the −125 to +250 µm coal fraction exhibited maximum ash removal. The T20 sample useful heating value increased from 8116 to 8203 kcal/kg and the T60 sample from 8060 to 8210 kcal/kg. X-ray diffraction and FTIR patterns showed mineral phases like quartz, kaolinite, and pyrite. The FTIR spectra indicated altered C-S, SO2, and C=O bonds. The thermal profile showed a 12.54% mass loss difference between untreated and treated coal samples, suggesting lower thermal stability post-treatment without affecting the useful heating value (UHV). The treated coal’s surface leaching and morphological structure changes were investigated using Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS) images. Raman analysis revealed increased carbon crystallinity and molecular structure in treated coal. This study offers an environmentally friendly and efficient approach to clean coal production.