<p>The uses of chemical fertilizers and pesticides have resulted into severe negative consequences to human health and the environment. Besides, there is growing demand by the consumers for organic and safer food products. In this context, endophytic fungi have been well recognized as eco-friendly alternatives to chemicals due to their numerous beneficial effects on plant growth and development. In this study, endophytic fungi were isolated from <i>Solanum pimpinellifolium</i>, a wild and underutilized tomato of North East India and determined for their plant growth promoting traits. Out of the total isolates, 17.86% showed indole-3-acetic acid (IAA) production, 39.28% solubilize phosphate, 39.28% were able to produce siderophores, 53.57% and 57.14% of the isolates assimilate ammonia and fix nitrogen respectively. Amongst them, two isolates identified as <i>Colletotrichum gloeosporioides</i> and <i>Penicillium sumatraense</i> showed promising PGP activity. A pot experiment conducted in greenhouse on cultivated tomato to evaluate the effect of the isolates on growth promotion ability significantly enhanced the growth and biochemical parameters of tomato plant as compared to the control. Further, experimented plant treated with <i>C. gloeosporioides</i> showed considerable increase in both the root and shoot lengths. GC-MS analysis of the fungal extract of <i>C. gloeosporioides</i> showed presence of IAA and other bioactive compounds. Purification of the fungal metabolites revealed presence of indole-3-acetamide (IAM) as a major pure compound. IAM is known to be the precursor of IAA in auxin biosynthetic pathway. Our study indicated that wild and underutilized crops harbour distinct endophytic fungi with immense potential for application as bioinoculants to increase crop productivity in sustainable agriculture practices.</p> Graphical Abstract <p></p>