Prokaryotes play crucial roles in the rehabilitation process to restore the ecological integrity of disturbed areas. This work reports on the profiles of N‐fixing microorganisms and Actinobacteria, from DGGE, the prokaryotic composition from next‐generation sequencing (NGS) and physicochemical soil characteristics. We compared a deactivated mining site where mining ended about 10 years ago, when the revegetation process was begun (RV), and a reference site, with natural vegetation (NT), both located at Retiro das Almas Mine, in the Quadrilátero Ferrífero region, Minas Gerais, Brazil. In both sites, the most abundant archaeal and bacterial groups included Euryarchaeota, Thaumarchaeota, Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia and revealed differences in their ecological metrics and distribution. Proteobacteria and Actinobacteria were most abundant in RV sites, while Acidobacteria and Verrucomicrobia were most abundant in NT sites. Less abundant phyla, such as Bathyarchaeota (Archaea) and GAL 15 (Bacteria) were found only in NT, while Gracilibacteria, Ignavibacteriae BJ‐169, and BRC1 were only found in RV. The majority of identified bacterial genera were shared by RV and NT. Soil P, pH, and particle density were most significant (p < 0.05) in RV, while Fe, Ca, organic matter, potential acidity and dispersed clays, were most significant (p < 0.05) in NT, showing differences in soil characteristics, which led the prokaryotic composition in these sites. DGGE profiles of N‐fixing microorganisms revealed N‐fixing predominance in both sites, although after 10 years prokaryotes diversity increased in RV site. Our results revealed that prokaryotic structure and composition are indicative of RV soil resilience.