Heterocycles are organic compounds that are well-known and distributed in nature; they can be used in the pharmaceutical, agrochemical, and chemical industries. Heterocycles composed of sulfur, nitrogen, and oxygen atoms are harmful toxins and can cause cancers; these substances can persist for years in the environment. One attractive alternative to expensive physical and chemical methods is microbial degradations, which present high potential and low cost, causing minimal environmental impacts. The use of these microorganisms makes use of heterocyclic substances as substrates, removing them efficiently and safely. Some strains of wild and genetically modified microorganisms (bacteria and fungi) have already been used to degrade various pesticides and aromatic compounds. Understanding the biodegradation mechanism of microorganisms will benefit future bioremediation studies, which may prove to be one of the alternatives to solving environmental problems. This review will focus on the microbial degradation of heterocyclic compounds, taking into account the most used techniques and their limitations in future research