Disclosed herein a process for upgrading the liquid hydrocarbon fuels by reducing aromatic content, sulfur content and nitrogen content wherein the process comprising isolating polycyclic aromatic hydrocarbon (PAH) transforming microbes and preparing biocatalyst by mutagenesis, contacting the biocatalyst with the liquid hydrocarbon fuel in an aqueous medium for transforming the aromatic, sulfur, and nitrogen containing compounds to polar substances, subjecting the mixture of biocatalyst and the liquid hydrocarbon fuel to a process of bioconversion, removing the polar substances by liquid-liquid extraction with a polar solvent to obtain dearomatized, desulphurised and denitrogenated liquid hydrocarbon fuel and recovering the upgraded liquid hydrocarbon fuel.