One of the main pathological problems for cropping sacha inchi (Plukenetia volubilis L.) is its susceptibility to root-knot nematodes (Meloidogyne incognita). In this study, fungal endophytes were explored in the stems and leaves of seven species of the Plukenetia genus, and also evaluated the abilities of isolates of Trichoderma and Clonostachys as biocontrol agents against damages caused by this nematode in sacha inchi. In order to evaluate such effects, seedlings were colonized with these fungal isolates, and then they were infested with root-knot nematode eggs. The results showed that the Plukenetia genus is rich in diversity of fungal endophytes. Their greatest diversity was found in Plukenetia brachybotria. Among the most efficient isolates for endophytic colonization, some of Trichoderma (e.g., kmd-36 and kmd-54) and others of Clonostachys (e.g., kmd-68 and kmd-80) provided a significant (p < 0.05) reduction in the number of galls induced by the nematodes, in comparison to the control treatment without endophytic colonization. In addition, these isolates allowed a better root development in the tested plants, thus revealing a good biocontrol potential against M. incognita in sacha inchi.