Although mycorrhizae applications have been widely used to improve the establishment and growth of agricultural crops, there have been no studies on their application in field-grown nectarine trees. In this work, a commercial arbuscular mycorrhizal fungus (AMF; Glomus iranicum var. tenuihypharum) was applied by means of fertigation to inoculate young “Flariba” nectarine trees grown in south-eastern Spain to evaluate its effect on plant water status, and vegetative and reproductive growth. Using minirhizotrons to measure the root dynamics over a complete growing season, revealed that AMF substantially increased root growth (51% increase compared with untreated trees), while no changes in plant water status or canopy development were noted. The productive response improved in inoculated trees, as demonstrated by a significantly higher yield, fruit size, number of fruits per tree and greater crop load efficiency values than in untreated trees. Given that the same amount of irrigation solution was applied in both treatments, the irrigation water use efficiency increased by 19.5% in AMF compared with untreated trees. The findings of this study suggest that a simple inoculation of AMF can be considered a good practice in semi-arid agro-systems to firmly establish efficient young nectarine trees and enhance their adaptation to field conditions.