Soil microbial communities are key regulators of ecosystem functioning in dryland environments, however, their taxonomic responses to land degradation and restoration in the Brazilian semiarid region remain poorly understood. This study aims to assess soil microbial taxonomic patterns in desertification nuclei of Irauçuba (CE) and Cabrobó (PE), and in the Cariris Velhos region (PB), in the Brazilian Northeast. We compared native vegetation (NV), degraded (DE), and restored (RE) areas under distinct pedoclimatic conditions and land-use histories. Soil samples were collected from the 0–10 cm layer following a factorial design with three areas, three management conditions, and six replicates per condition, totaling 54 samples. Shotgun metagenomic sequencing was performed to characterize soil microbial communities. To this end, the samples underwent quality control using FastQC, followed by filtering and adapter removal with Trimmomatic. The taxonomic profile of the microbial communities was inferred based on taxonomic markers using the mTags tool. The microbial community composition at the phylum level was largely dominated by Actinobacteriota across all areas and treatments evaluated. Differences in the relative abundance of other phyla were observed among land uses, with NV showing a higher proportion of groups associated with more stable soils, such as Proteobacteria and Acidobacteriota, while DE exhibited a greater predominance of stress-tolerant phyla, such as Firmicutes. RE displayed an intermediate pattern. In addition, regional variations were evident, indicating that microbial community responses to degradation and restoration are dependent on local conditions. Degradation simplifies the microbial community, whereas restoration promotes partial recovery, still distinct from native vegetation.