Aims <p>This study aimed to evaluate the diversity of endophytic fungi in <i>Fagopyrum dibotrys</i> and investigate their plant growth-promoting (PGP) traits and mechanisms influencing the growth and development of Tartary buckwheat (<i>Fagopyrum tataricum</i>). Methods: A total of 95 endophytic fungal isolates were identified. Among them, J2 (<i>Alternaria alstroemeriae</i>) and J62 (<i>Alternaria solani</i>) exhibited strong PGP activities, including the production of potassium, indole-3-acetic acid (IAA), and iron chelators. The growth-promotion effect was most pronounced when these strains were co-cultured with Tartary buckwheat.</p> Results <p>The results demonstrated that the two endophytic fungi significantly enhanced plant height, fresh weight, dry weight, and the number of lateral roots in Tartary buckwheat plants. Additionally, a notable increase in photosynthetic efficiency, antioxidant enzyme activity, chlorophyll content, as well as soluble sugar and protein levels, was observed in the leaves of Tartary buckwheat. Furthermore, the levels of flavonoids and phenolic compounds in the leaves and seeds of Tartary buckwheat showed a significant increase. Transcriptomic and metabolomic analyses revealed that J2-colonized Tartary buckwheat primarily promoted plant growth by enhancing photosynthetic processes, while J62-colonized plants exhibited increased anthocyanin biosynthesis. The enhanced diversity and high concentration of phenolic compounds contributed to improved systemic resistance in Tartary buckwheat, thereby promoting its growth and development under adverse environmental conditions.</p> Conclusions <p>In conclusion, these two plant growth-promoting endophytic fungi possess diverse PGP traits, suggesting their potential application as biofertilizers or plant growth regulators.</p>