Soil, the supporter of life and the home to all living beings, stores nutrients, supports plant growth and the living space of various microflora; presently, due to the overuse of pesticides, fertilisers, herbicides, etc., contamination of soil has become a major concern globally. Although there have been methods to control and remove the recalcitrant compounds from soil, we still need newer technologies, which are efficient and applicable in recycling most of the pesticides. As microorganisms are ubiquitous, they can survive in various habitats, utilise various substrates, and possess the ability to produce various enzymes. This property of microorganisms is exploited by humans to treat soil contaminated with recalcitrant compounds. The current book chapter focuses on various fungi and their enzymes involved in the treatment of contaminated soil.