The distribution of plant communities in hot desert ecosystems is discontinuous and resembles the pattern of heterogeneous resource patches, known as “fertility islands”. Understanding the key factors that allow plants to establish in these conditions, as well as their associated microbial diversity, is crucial to the comprehension and preservation of these ecosystems. Saudi Arabia in the Arabian Peninsula, is one of the driest regions in the world, with a very low water regime and low soil nutrient contents. The establishment of ecosystems in these arid desert conditions is therefore subject to numerous constraints. Understanding the biotic and abiotic factors linked to the formation of fertility islands, from the perspective of soil composition and its associated microbiome, both in the soil and in the roots of associated plant community, is therefore a fundamental issue for the preservation of these ecosystems. In this study, we analyzed the soil composition between a fertility island and bare soil. The proportions of micro- and macro-elements important for plant nutrition, namely magnesium, phosphorus, potassium and iron were higher in the fertility island. We also observed that soil bacterial and fungal diversity increased in the fertility island. Key taxa such as Rhizobia and Glomeraceae which play important roles in ecosystem functioning were identified in both the fertility island soil and in the roots of the established plant community. These results confirm that plant establishment is linked to soil conditions, in line with the fertility island hypothesis, and that the microbial community in the fertility island differs both in diversity and in composition from that of the bare soil. Fertility islands soils and the roots of established plant community harbor a microbiome potentially crucial to ecosystem functioning, and are of major interest for conservation and agronomy programs.