Agricultural practices are known to affect the diversity and efficiency of arbuscular mycorrhizal fungi (AMF) in improving overall plant performance. In the present study we aimed to compare the abundance, richness, and diversity of AMF communities under organic farming of a desert ecosystem in the Arabian Peninsula with those of an adjacent conventional farming system and native vegetation. In total, 12 sites, including six plant species, were sampled from both farming systems and the native site. Spore morphotyping revealed 24 AMF species, with 21 species in the organic farming system, compared to 14 species in the conventional site and none from rhizosphere soil of a native plant (Tetraena qatarensis). The AMF spore abundance, species richness, and Shannon–Weaver diversity index were high under organic farming. In both systems, the AMF community composition and abundance associated with different crops followed similar trends, with pomegranates having the highest values followed by limes, grapes, mangoes, and lemons. Our results show that organic farming in such a desert ecosystem promotes AMF diversity.  These data imply that AMF might play an important role in the sustainable production of food in resource-limited desert habitats.