Background: Desert steppes and other arid and semi-arid ecosystems are highly susceptible to degradation. Revegetation has become a key strategy for improving soil quality and maintaining biodiversity. However, its effects on soil microbial diversity, community structure, and stability of microbial interdomain networks are still unknown, especially in arid restoration ecosystems. Methods: The study focused on Ningxia's desert steppes, examining the influence of revegetation with three plants-Sophora alopecuroides, Cynanchum hancockianum, and Artemisia ordosica-on soil physicochemical properties, microbial diversity, and stability of microbial interdomain networks. High-throughput sequencing was employed in analysing the bacterial and fungal community characteristics of the soil. Results: The results indicated that revegetation has the potential to significantly increase soil nutrients and enzyme activities, with C. hancockianum providing the most improvement effects. Revegetated soils had lower microbial diversity relative to bare soils, and microbial communities were shifted to a copiotrophic microbial community structure dominated by Proteobacteria and Bacteroidetes. Furthermore, the stability of microbial interdomain networks in revegetated soil, particularly those influenced by Cynanchum hancockianum, was markedly decreased. Conclusions: The findings indicate that although vegetation restoration can improve soil quality, it also alters the dynamics of microbial communities and reduces network stability, emphasising the need for careful species selection and long-term monitoring in restoration practices.