To increase the analytical precision in identifying structural forms of heavy metals, it is necessary to refine the methodology for analysis of mineral crystals. The aim of this study was to characterize clay crystals in soils, and relate their mineralogy to the structural occurrence of Pb using scanning transmission electron microscopy (STEM) together with energy dispersive X-ray (EDX) spectrometry. We sampled soils from two areas naturally rich in heavy metals, with known occurrences of mineral deposits (PbS) in carbonate and phyllite/mica schist rocks. There was an association of P with Pb, and the main mineral phase containing Pb in the soil clay fractions was plumbogummite. No associations between Pb and Fe oxides were observed. Secondary phyllosilicate minerals, such as kaolinite and smectite, did not contain structural Pb. There was isomorphous substitution of Ti by Pb in an anatase crystal, despite the differences in ionic radii. The chemical analysis of individual crystals by STEM-EDX was hampered by the high occurrence of microaggregates of clay minerals.