Soil microbiome plays an important role in soil forming process as well as soil functioning. This is especially relevant for initial stages of soil regeneration after strong anthropogenic impact (i.e., in quarrying complexes). The study of soil microbiome in such areas is crucial for both understanding the forces driving soil formation and optimization of the reclamation techniques. This study is aimed to investigate the soil microbiome of different ages of soil formation on the heaps of limestone mines in conditions of boreal climate of North-West of Russia. Soil microbiome analysis was performed using high-throughput sequencing. Soils of the investigated sites were predominantly Rhendzic Leptosols. The initial set (2 years) of OTUs in the entire period of soil formation remains unchanged, accumulating more than 98% of the total microbiome in each time point. Analysis of beta-diversity (weighted and unweighted) demonstrated a clear differentiation of microbiomes of all time points, which suggests that underlying taxonomic structure variations can be attributed to variation of the minor taxa set composition. The most significant differences occur in Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria, but majority of these phyla have different sets of OTUs demonstrating opposite trends. Generally time positively correlate with microbiome of carbonate soils in all cases of benchmark and newly formed soils is familiar because of the uniform zonal environmental conditions in geochemically specific landscape of Izhora upland.