Desertification is a major driver of land degradation in global drylands, resulting in losses of above- and below-ground biodiversity. Although soil microorganisms are essential for ecosystem functioning, their responses to desertification across contrasting environmental contexts remain insufficiently understood. Here, we conducted a cross-regional assessment of how desertification reshapes soil fungal communities across four major desertification nuclei in the Brazilian semiarid region. Within each nucleus, we compared native vegetation, degraded soils, and restored areas under distinct restoration strategies using high-throughput ITS metabarcoding. Fungal communities were consistently dominated by Ascomycota (∼80%) across nuclei; however, degradation induced pronounced compositional turnover at finer taxonomic resolution and promoted more uneven, stress-associated assemblages. Alpha diversity responses were inconsistent across regions, whereas beta diversity revealed significant separation among native, degraded, and restored soils in all nuclei. Degraded areas generally exhibited higher proportions of habitat specialists and reduced generalists, indicating niche contraction and patterns consistent with intensified environmental filtering, although this pattern varied among sites. Functional guild composition was also reorganized, with region-specific shifts among saprotrophic, pathogenic, and symbiotic groups. Overall, desertification restructures soil fungal communities across taxonomic, niche, and functional dimensions, while restoration leads to partial but context-dependent reassembly rather than full convergence toward native states. These findings position soil fungal communities as sensitive, multidimensional indicators of dryland degradation and provide a regional framework for monitoring microbial responses under desertification pressure.