In tree-based intercropping systems, roots of trees and crops are interacting and could influence ecosystem services provided by soil microorganisms. Here, the analysis of diversity of arbuscular mycorrhiza fungi (AMF) associated with roots of walnut and maize reveals differences. Of interest, Funneliformis genus is mainly associated with maize roots, and one OTU related to an uncultured Glomus, might form a common mycorrhizal network linking roots of both plants. In addition, the analysis of 13C of mycelium living in the surrounding environment of roots, suggest that part of the carbon derived from walnut trees could be transferred to maize plants. Our results suggest that in temperate agroforestry ecosystems, AMF could participle in the redistribution of nutrients between connected plants.