Deserts are home to diverse microbial communities important in many ecological processes and strategies for responding to a changing climate. We recorded the biodiversity of soil-inhabiting fungi and their predictors in Saudi Arabia via metabarcoding. Alpha diversity of the fungal communities varied greatly, with high diversity in moist montane habitats and very low diversity in hyper-arid regions. The fungal community was dominated by members of the orders Pleosporales, Pezizales, Agaricales, Glomerales, and Sordariales, most of which represented saprotrophic guilds. Modelling analyses showed that soil pH, elevation, vegetation coverage, and vegetation indices substantially impact soil fungal richness and community composition. These patterns mirror global dryland trends, with low diversity and high evenness in hyper-arid sites but higher richness and ecological differentiation in montane and vegetated regions. Our results demonstrate that vegetation cover, edaphic conditions, and altitude jointly shape fungal diversity in Saudi Arabian soils, offering mechanistic insight into community assembly and predicting ecosystem responses to climate change in arid landscapes.