Arbuscular mycorrhizal fungi (AMF) contribute to plant health management, especially in bioprotection against soil-borne pests such as root-knot nematodes (Meloidogyne spp.). These worldwide spread pests have a particularly severe impact on vegetable crops. Our aim is to combine AMF and companion plants as agroecological means to reduce root-knot nematodes impact. Firstly, we assessed the companion plants ability to promote native AMF diversity by using metabarcoding analysis. Secondly, the bioprotective effect of AMF was associated with a nematode-repulsive companion plant: Tagetes patula. The study was conducted under greenhouse conditions on a susceptible pepper cultivar (Capsicum annuum cv Doux Long des Landes) by comparing two AMF stimulation strategies. The first one involved the use of a standardized commercial inoculum composed of two strains of AMF (Funneliformis mossae and Rhizophagus fasciculatus), whereas the second aimed to enhance the diversity of native AMF before planting the peppers, by intercropping a mycorrhizotrophic plant: Crotalaria spectabilis. We then evaluated the bioprotective effect of the association of T. patula and the AMF communities on the nematodes-infected peppers. The promotion of native AMF was more efficient than using the commercial inoculant to induce the mycorrhization of the peppers. The association of T. patula with mycorrhized peppers resulted on an average reduction of root-knot nematodes infections on peppers by 72%. T. patula showed a good potential both for its bioprotective effect and its ability to promote native AMF diversity. These results call for further studies under controlled conditions over a longer time period before being conducted in the field.