Soil microorganisms play a central role in biological soil functioning. One of the beneficial microbiota that have a symbiotic association with most of the plants is arbuscular mycorrhizal fungi (AMF). Nevertheless, the influence of soil bioindicators in plants response to mycorrhizal colonization is still poorly documented. The impact of cover crops, widely used in conservation agriculture or organic farming on native mycorrhizal fungi, is little known. In order to find whether native AM fungal community associated with walnut trees is influenced by soil bioindicators, root, rhizosphere soil samples and technical itineraries were collected from the agroforestry plots in Dordogne and the experimental station of Creysse (South-western France). Five modalities (Walnut in Conventional with and without vegetal cover, Walnut in Organic farming with and without vegetal cover, Walnut and maize in Agroforestry) and soil physico-chemical and biological analyses were studied. Our results showed a higher mycorrhizal colonization in walnut trees in organic farming in comparison with those in conventional farming. Whatever the modality, the highest percentage of total AMF colonization was recorded for walnut trees in the presence of faba bean. Multivariate analysis based on principal component analysis revealed that only the ergosterol content was mainly correlated to mycorrhizal colonization and hence relevant to explain walnut trees mycorrhization. The use of faba bean showed the great role played by vegetation cover in the enhancement of 63 mycorrhizal colonization of plants. Identification of the functional traits of mycorrhizal fungi sensitive to walnut trees is required to inform decisions in specific agricultural practices