Fungal secondary metabolites are low molecular weight (or bioactive) compounds synthesized by fungi not as a component of the more basic metabolic processes, but possibly with diverse bioactivities. They have diverse biological activity, including antioxidants, antimicrobial activity, anti-anti-inflammatory activity, and are used in many spheres, such as agriculture, cleaning the environment, medicine, human health, and so on. These metabolites are extremely crucial to the ecology of the fungi, like their self-defense mechanisms against other organisms, their food, and their association with plants. They are significant in environmental management such as the phytoremediation of the environment, plant growth, resistance to diseases, minimizing the utilization of synthetic pesticides. The fungus can be more widely used in improving the soil health, plant growth, and biocontrol agent in agriculture through the secondary metabolites produced by the useful fungi. In addition to this, fungal secondary metabolites play an important role in environmental control in the breakdown of toxic substances including organic xenobiotics and heavy metals. The chapter has provided an introduction on different environmental applications of fungal secondary metabolites that comprise bioremediation, biocontrol, generation of bio-based products, ecosystem restoration, better soil quality, plant growth, and sustainable waste management, etc.