Research highlights: this article refers to the deep storage of trace elements as a result of the podzolization process under different types of vegetation cover. This is also an attempt to trace differentiation in the distribution of trace elements in mountain soils under the podzolization process. Background and objectives: we focused on estimating whether the podzolization process of soils under various vegetation covers led to the deep storage of trace elements in the subsoil. Furthermore, the potential contamination of studied soils with trace elements using pollution indices was assessed. Materials and methods: in thirteen soil profiles under three different vegetation types, chosen chemical–physical properties, e.g., organically bonded and active forms of Al and Fe, podzolization indices, and trace element content (Cd, Pb, Zn, Cu, Cr, and Ni) were analyzed. Additionally, pollution indices, such as Geoaccumulation Index, Potential Ecological Risk, Pollution Load Index, and Contamination Security Index, were calculated. Results: the distribution of Al and Fe varied among the soil profiles, suggesting different rates of podzolization processes that were partially dependent on the type of vegetation. Exceptionally high values of Alo and Feo were noted in profiles P1 and P2 (1.53% and 2.52% for Alo, and 2.13% and 1.46% for Feo, respectively) in horizons Bs and BsC under Plagiothecio-Piceetum taricum. Some of the soils showed the expected distribution of trace elements as the result of the podzolization process revealed their accumulation in the spodic horizon. Moreover, four different patterns of trace element distribution were recognized. Often, the accumulation of trace elements occurred in Bs/BsC horizons, e.g., in case of Zn soils P8, P9, and P10, which reached 65.8, 68.0, and 72.30 mg∙kg−1, respectively. However, there were no large differences in trace element content in soils independent of the vegetation type. The pollution indices in most samples confirmed lack of contamination with trace elements. Only several soil horizons were moderately polluted and showed deterioration of soil quality or very low severity. Conclusions: in the majority of studied soils, the podzolization process resulted in the deep storage of trace elements, i.e., the accumulation of spodic horizon; however, in certain cases, it might have been related only to the different lithology, and appeared as anomalies not related to the dominant soil-forming process. Anomalies were characterized by a much higher content of trace elements in the BsC horizon compared to the upper O horizons. Obtained data of trace elements, as well as values of pollution indices, did not indicate pollution. This lack of pollution was related to localization of soils within a topographic barrier that protected them from the deposition of potential trace element–rich pollution.