The study of chronosequences allows the analysis of the temporal and spatial dynamics of ecogenesis, soil microbiome and soil development. Here, we investigated the taxonomic diversity of bacterial and archaeal communities along a chronosequence of soils that formed on four Lake Ladoga coastal bars in the Nizhnesvirsky Nature Reserve (Leningrad region, north-west Russian Federation). We analyzed two factors: the age of sampled solum (ranging from 70 to 1,590 years) and the soil horizons that differ in terms of morphology and genesis. We observed a relationship between podzolisation, typical major soil-forming processes of the southern taiga zone, and the taxonomic structure of prokaryotic communities. The most pronounced differences between microbial communities were associated with the vertical heterogeneity of soil profile. Phyla associated with copiotrophic habits (Proteobacteria, Actinobacteria and Bacteroidetes) were more frequent in topsoil. Podzolic eluvial (E) horizons had higher frequencies of the genus Mycobacterium (Actinobacteria). In deeper horizons, we observed lower frequencies of copiotrophic phyla and increased frequencies of phyla associated with oligotrophic habits (Nitrospirae, Gemmatomonadetes, Planctomycetes, Chloroflexi, etc.), as well as archaeal lineages. The lowest (gleyic, G) horizons had high frequencies of anaerobic and methane-producing bacteria. Therefore, the relationship between microbial community structure and the continuous development of the soil profile was revealed. Shifting physico-chemical were identified as key factors associated with variation in prokaryotic communities. The older coastal bar demonstrated the clearer signs of podzol formation, increased thickness of the E horizon, and increased differentiation among microbial communities in different genetic horizons.