The Urals (Russia) are among the largest mining areas in the world, with millions of tons of mine waste deposited. An old sulfidic tailing dump formed over decades of mining activities at the Sibay ore-processing plant is a typical cause of acid mine drainage (AMD) formation, posing a threat to ecosystems of neighboring environments. In this study, the formation of oxidized surface soil layers in four zones of the Sibay tailing dump was revealed, and their chemical–mineralogical and physical–mechanical characteristics were analyzed. According to the results of the metabarcoding of hypervariable regions of the 16S rRNA genes, oxidation in soil layers was associated with the activity of sulfur- and iron-oxidizing acidophiles represented by a few genera: Ferroacidibacillus, Sulfoacidibacillus, Sulfobacillus, and Ferroplasma. The structure of the microbial communities in soil layers differed depending on the zone and depth of sampling. In the samples characterized by the weak oxidation of sulfide minerals, microbial communities were dominated by bacteria of the genus Pseudomonas. The data obtained in this research are of importance to predict the oxidation/leaching processes in mine wastes and their negative environmental impacts in the mining region, as well as to develop technologies for processing these raw materials.