A wide program of fruit tree planting, notably jujube trees, has been implemented in the framework of the panAfrican Great Green Wall (GGW) project to improve food security in arid and semiarid regions. However, the success of such initiatives is highly limited by a low tree growth and high tree mortality rates due to transplant shocks from tree nursery to field. The positive impact of mycorrhiza-based ecological engineering strategies on jujube trees were previously demonstrated in nursery conditions, but field monitoring is necessary to evaluate their sustainability in terms of plant growth and survival. In the current study, local (Tassel) and exotic (Gola) jujube cultivars were tested for their response to mycorrhizal inoculation with the non-native arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis IR 27 and fertilization with rock phosphate. The environmental impacts of both treatments were assessed by characterizing the native AM fungal community in a 13-month-old jujube orchard. Field results demonstrated higher rates of survival and a relative stability of nursery-driven plant benefits of inoculated jujube trees, as well as a potential higher persistence of AM fungal inoculum for the exotic cultivar. The native AM fungal community associated with the local cultivar was the most diverse, but Glomeraceae was predominant in both cultivars. The mycorrhiza-based ecological engineering strategies proposed in this work affected both AM fungal communities, notably Glomeraceae and Gigasporaceae members, but in a higher extent for the local jujube cultivar. Results highlight the strong benefits of mycorrhizal inoculation at the very early stages of tree seedling growth in nursery and their stability in the first year of plantation. Nevertheless, a deeper assessment of mycorrhizal inoculum persistence and spread, and a wider characterization of soil and root microbiome need to be implemented in further field monitoring to better evaluate the environmental impacts.