Heterocyclic sulfur-containing hydrocarbons and aromatic amines are major pollutants in fossil fuels and wastewater from the petroleum and dye industries. The Clean Air Act of 1990 mandates sulfur removal from fossil fuels and wastewater. Bio-desulfurization using ligninolytic enzymes, such as manganese peroxidase, is feasible. The enzyme demonstrated the highest efficiency in degrading sulfur-containing hydrocarbons, including ortho-toluidine, a hazardous amine. The MnP biocatalyst demonstrated 92%, 98%, and 70% removal efficiencies for dibenzothiophene, benzothiophene, and ortho-toluidine, respectively. Different metabolites of the degradation were confirmed by IR spectroscopy, thin-layer chromatography, and GC-MS analysis. The biodegradation method for dibenzothiophene, using 4S and Kodama pathways, is highly efficient and environmentally friendly. The study found that MnP more efficiently degrades sulphur containing organic pollutants than nitrogen containing ortho-toluidine. The stability of aromatic compounds was disturbed by the presence of an electron-rich sulphur atom. Hence DBT and BT, are more susceptible to oxidative cleavage than ortho-toluidine.MnP biocatalysts have high catalytic activity efficiency, but many are not used in large-scale industrial applications. Future challenges lie in developing versatile biocatalysts using genetic engineering, proteins, surfactants, purified enzymes, and high-resistant strains.