Revegetation is widely used to restore degraded dryland ecosystems; however, soil microbial communities and functionality may reverse in late succession after long-term shrub plantations. To assess the impacts of long-term restoration on soil microbiome, we tracked diversity, community composition, network complexity, and their functionality of soil fungal and bacterial communities along a 50-year revegetation chronosequence of shrub revegetation at two ecologically distinct sites in northern China. We found that the dominant soil microbial taxa shifted from fungal symbiotrophs to pathotrophs during intermediate stages (i.e., 20-30 years), considerably earlier than shrub degradations in late stages (40-50 years). This shift was mainly driven by increase in soil nutrient availability and completion between pathotrophs and symbiotrophs for shared resources. Changes in microbial composition associated with a transition in microbial co-occurrence networks, which showed reduced complexity and fewer associations among dominant taxa at intermediate stages. Furthermore, changes in fungal composition and network structure negatively affected soil functionality at both sites. By incorporating two contrasting sites, our results highlight the preceding role of fungal pathotrophs in the degradation of revegetated shrub. They provide robust evidence that long-term shrub revegetation may inadvertently undermine soil microbial health and resilience.