Fabaceae is considered the third largest family of the plant kingdom, comprising of a large number of plants, belonging to 650 genera and 20,000 species of plants. Out of the various plant species that are reported in the family Fabaceae, many of the species have been reported to exhibit diverse pharmacological activities and are of economic importance to agriculturists and scientists across the globe. Studies over the last few decades have unraveled a lot of concrete information about different plants, ranging from the mutualistic interdependence of plants and microbes for their survival to the innumerable benefits of plants in the sectors of agriculture, food industry, medicine, and healthcare. The survival and effective maintenance of plant homeostasis is largely regulated by the diverse microbial population that co-exists in symbiotic relationships with plants. This endophytic microbial population can be either categorized as endophytic bacteria or endophytic fungi. The studies over the past decades have highlighted the crucial role of both endophytic bacteria and fungi in the growth and development of plants. This review explores the ameliorative roles of endophytic fungi in alleviating biotic and abiotic stresses in plants. Additionally, it highlights the vast diversity of secondary metabolites produced by these fungi and their potential applications. Secondary metabolites exhibit a wide range of biologically significant activities, including anticancer, antimicrobial, antimalarial, and nematicidal properties, which hold substantial importance in therapeutic and agricultural applications. Furthermore, the role of various endophytic fungi of the Fabaceae family has been shown in phytoremediation.