Endophytic fungi play a crucial role in plant habitat adaptation, enhancing productivity and protecting against biotic and abiotic stresses. The benefits of endophytic colonization arise from both direct effects, such as phytohormone synthesis, and indirect effects, including the production of secondary metabolites and antibiotics, induced resistance, and protection from various stressors. In addition to protecting plants from pests and diseases, certain fungal endophytes have been utilized to reduce animal toxicity associated with these fungi in temperate grasses, enhance the cultivation of maize and rice plants tolerant to a range of biotic and abiotic stresses, and improve post-harvest control management. The loss of fungal endophyte diversity in domesticated plants can result from various practices, such as plant breeding and seed treatments, often due to a lack of awareness of the importance of fungal endophytes. This may explain why some endophyte strains are less effective at conferring benefits to plants. We offer recommendations for mitigating these negative effects in modern agriculture.