This paper reports the results of a geochemical study focused on the distribution of heavy elements (As, Cd, Co, Cr, Cu, Ni, Pb, Sb, Tl, U, Zn) in soil profiles, with the aim of defining their geochemical background, contamination threshold, surface and vertical extent of contamination in soils of a metallurgical and industrial area in Kosovo. The geochemical background of heavy elements in soil was assessed by exploratory data analysis of their concentrations in soil profiles, and the contamination threshold was used as reference value to quantify their anthropogenic enrichment. Cadmium, Pb, Sb, Zn were the primary soil contaminants, As, Cu, Tl the secondary ones. The main sources of soil contaminants were the Zvecan smelter for Pb, Sb, As, Cu, Tl, and the Trepca industrial complex for Cd and Zn. The highest levels of Pb and Sb contamination were found up to depths between 30 and 60 cm in soil profiles within 5 km north and south-east of the Zvecan smelter. Contamination by Pb and Sb decreased with depth in soil profiles and affected the whole thickness of soils closer the metallurgical plant. Cadmium and Zn contamination declined with distance from the Trepca industrial complex and decreased with depth, generally extending down to depths of 40–90 cm and 30–70 cm, respectively. Cobalt, Cr, Ni, U were geogenic heavy elements. Anomalous natural concentrations of Co, Cr, Ni were found in soils collected in the northern part of the study area, where the geology consists mainly of ultrabasic and basic magmatic rocks.