Activities connected to mineral mining disrupt the soil layer and bring up to surface parent rock material. As a result, they leave behind vast areas of disturbed lands, that are difficult to restore due to altered environmental conditions. Returning these lands to the natural ecosystems is an important contemporary challenge. Soil microbiome composition reflects changes happening to disturbed lands, its analysis helps to evaluate disturbance degree and estimate the effect of implementation of remediation techniques. Also, factors connected to the characteristics of a particular geographical region have a certain impact and should be taken into account. We focus on microbiomes of disturbed lands from two sandy-gravel mining complexes in mountainous areas with moderate continental climate of Central Caucasus. These quarries share the same parent rock material but differ in benchmark soil type and presence of remediation practices. Comparative analysis of microbiome composition based on sequencing of 16S rRNA gene libraries showed that region and disturbance are the key factors explaining microbiome variation, which surpass the influence of local vegetation factors. However, application of remediation techniques greatly reduces dissimilarity of soil microbiomes caused by disturbance. Linking of soil agrochemical parameters to microbiome composition showed that disturbance factor correlates with a lack of organic carbon. Other agrochemical parameters, like pH, ammonium, nitrates and total carbon explain variation of microbiomes on a smaller scale between sampling sites. Thus, while regional and disturbance factors reflected differentiation of soil microbiomes, soil agrochemical parameters explained local variation of certain groups of microorganisms.