The Caatinga, a semiarid Brazilian biome, is the largest tropical dry savanna forest in South America. With a high environmental heterogeneity, it has a great complexity of communities and endemic species. Among the microorganisms found in the Caatinga, arbuscular mycorrhizal fungi (AMF) form symbiotic associations that increase nutrient absorption and the tolerance of plants to biotic and abiotic stresses. This study aimed to determine the structuring factors of AMF communities across three Caatinga ecoregions (9 areas in total), which differ in soil and vegetation: Northern Sertaneja depression (shrub & tree savanna), savanna-forest Borborema Plateau (most humid and elevated), and dry shrubland Raso da Catarina. These hypotheses were tested: (1) AMF communities differ in composition and structure among the ecoregions; (2) Raso da Catarina has the greatest AMF richness and diversity; (3) edaphic factors (pH and phosphorus content) are key determinants for differences among AMF communities. Multivariate analyses showed that richness, diversity, and composition of AMF communities differed among the ecoregions, represented by 73 species of 19 genera, predominantly Acaulospora, Glomus, and Rhizoglomus. The Northern Sertaneja depression had greater richness, diversity, and abundance of spores than the other areas. Soil moisture, aluminum, calcium, pH, sum of bases, and silt were the structuring elements of these AMF communities. This study highlights the importance to better understand the ecological aspects in the Caatinga ecoregions related to AMF, providing scientific bases for conservation strategies to protect these symbionts, which are fundamental to the resilience of semiarid ecosystems in the face of climate change.