Sulfur (S), nitrogen (N) and oxygen (O) heterocycles areamong the most potent environmental pollutants.Microbial degradation of these pollutants is attractingmore and more attention because such bioprocesses areenvironmentally friendly. The biotechnological potentialof these processes is being investigated, for example, toachieve better sulfur removal by immobilized biocatalystswith magnetite nanoparticles or by solvent-tolerantbacteria, and to obtain valuable intermediates fromthese heterocycles. Other recent advances have demonstratedthe mechanisms of angular dioxygenation ofnitrogen heterocycles by microbes. However, these technologiesare not yet available for large-scale applicationsso future research must investigate proper modificationsfor industrial applications of these processes. Thisreview focuses on recent progress in understanding howmicrobes degrade S, N and O heterocycles.