In 1866, De Bary proposed the concept of “endophytes” which are microbes exhibiting symbiotic, probably mutualistic relationships with several wild and cultivated plant species. It is established that factors such as geographical location, agricultural practices, environmental conditions, plant genotype, leaf position, growth stage, cultivars, etc. contribute to the fungal and bacterial endophyte community. The focus of this chapter remains on studies on fungal endophytes in wheat with reference to the diversity, ecological roles, and potential applications, particularly for maintaining plant health and productivity. Studies on plant growth-promoting, biocontrol, stress alleviating, and micronutrient mobilizing activities are valuable for sustainable agricultural practices aimed at reducing the reliance on synthetic growth regulators, chemical fertilizers, insecticides, and pesticides and improving overall plant health. Particularly, the seed-associated microbiota shows vertical transfer, and coadaptation with the host over generations and establishes a healthy crop stand. With the advances in sequencing technologies and microscopic techniques, in-depth studies on fungal endophytes can be undertaken for ensuring sustainable agricultural practices and food security for the future.