Since the 12th century in the Silesian-Cracovian area, lead, litharge, and silver have been produced by the pyrometallurgical processing of Pb-Ag-Zn ore. Slags and soils contaminated with heavy metals (Zn, Pb, Cd, Fe, Mn, As) were the subject of this research. Samples were collected during archaeological works in the area of early medieval metallurgical settlement. The main goals of the analyses (Scanning Electron Miscroscopy-Energy Dispersive Spectroscopy (SEM-EDS), Electron Probe Microanalyzer (EPMA), X-ray diffraction (XRD), Atomic Absorption Spectroscopy (AAS)) were the determination of the mineralogical composition of furnace batches and smelting temperatures and conditions. In soils, the anthropogenic phases enriched in Pb, Zn, Fe, Mn, P, and primary minerals like goethite, ferrihydrite, sphalerite, galena, smithsonite, minrecordite, cerussite, gypsum, anglesite, jarosite, and hemimorphite were identified. The soil from former metallurgical settlements contained up to 1106 mg·kg−1 Pb, 782 mg·kg−1 Zn, 4.7 mg·kg−1 Cd in the fine fraction. Much higher heavy metal concentrations were observed in the waste products of ore rinsing, up to 49,282 mg·kg−1 Pb, 64,408 mg·kg−1 Zn, and 287 mg·kg−1 Cd. The medieval smelting industry and Pb-Ag-Zn ore processing are marked by highly anomalous geochemical pollution (Pb, Zn, Cd, Fe, Mn, Ba) in the topsoil. The methods of mineralogical investigation, such as SEM-EDS or EMPA, can be used to identify mineralogical phases formed during metallurgical processes or ore processing. Based on these methods, the characteristic primary assemblage and synthetic phases were identified in the area polluted by medieval metallurgy and mining of Pb-Ag-Zn ores, including MVT (Mississippi Valley Type) deposits. The minerals distinguished in slags and the structural features of metal-bearing aggregates allow us to conclude that batches have included mostly oxidised minerals (PbCO3, ZnCO3, CaZn(CO3)2, FeOOH), sulfides (PbS and ZnS) and quartz (SiO2). The laboratory experiment of high-temperature heating of the examined slags showed that smelting temperatures used in the second half of 13th century were very high and could have reached up to 1550 °C. The results indicate, that geochemical and mineralogical methods can be used to obtain important information from archaeological sites, even after archaeological work has long ceased.