The microbiome of initial soils formed at the heaps and bottoms of surface sediment quarries in the surroundings of Yakutsk City (Eastern Siberia, Russia) has been characterized for the first time. In the initial Entisols, we detected Alphaproteobacteria (represented mainly by the family Rizobiales), Gammaproteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes (mostly Chitinophagales), Deltaproteobacteria, and Chloroflexi. The lower soil horizons had a more homogenous species diversity taxonomy that was dominated by Gammaproteobacteria. The morphologically different horizons did not differ microbiologically. This is caused by the limited soil development and relatively slow rate of revegetation of the spoil banks and heaps of the quarries under the severe climatic conditions of the Eastern part of Russian Arctic zone. Based on our findings, we propose that the soil microbiomes in such recently abandoned quarries are characterized by low diversity, which is a characteristic feature of the polar soils surrounding Yakutsk. Data obtained can be used for elaboration of reclamation strategies with taking into account the information about key microbial drivers of soil processes.