Soil microbial biodiversity plays a fundamental role in regulating dryland ecosystem multifunctionality, being influenced by various environmental factors, particularly plant cover and soil properties. However, the complex interactions among soil microbial communities, plant communities, and soil physicochemical properties in desert steppe ecosystems remain inadequately understood. To address this knowledge gap, we examined the relationships between aboveground plant communities and soil environmental parameters (including nitrate nitrogen, pH, cation exchange capacity, and effective phosphorus) and their influence on the diversity and community structure of soil bacteria, archaea, and fungi across 37 desert steppe sites in a typical northern China’s dryland region. Our results showed that bacterial diversity exhibited significant variation among plant communities, with notably higher diversity in Stipa breviflora-dominated soils compared to Peganum harmala-dominated soils. The microbial communities were characterized by dominant phyla: Acidobacteriota (21.5%) in bacteria, Crenarchaeota (97.3%) in archaea, and Ascomycota (82.1%) in fungi. Bacterial diversity was significantly correlated with soil pH, available potassium, and carbonate content, while archaeal diversity showed strong correlations with ammonium nitrogen, available phosphorus, carbonate content, and cation exchange capacity. Fungal diversity, however, exhibited significant correlation only with available phosphorus. Environmental factors explained varying degrees of community structure variations, with the highest explanatory power for archaea (66.1%), followed by bacteria (49.0%) and fungi (32.8%). Structural equation modeling revealed that plant communities influenced bacterial communities primarily through modifications in soil pH and cation contents. These findings underscore the critical role of plant communities and soil properties in shaping soil microbial diversity patterns. Given the essential function of biodiversity in ecosystem processes, we propose that soil microbial diversity serves as a valuable indicator for monitoring and assessing degradation in desert steppe ecosystems.