Post-mining waste from Zn-Pb ore exploitation undergoes processes of spontaneous succession and changes in soil chemical composition. The Zakawie area was industrially transformed by historical mining activity, ore enrichment, and the metallurgical processing of Zn-Pb ore. The subject of the study was to analyse the rate of vegetation succession (from 1999 to 2019), soil chemistry, and the relationships between them in an anthropogenic habitat with high concentrations of potentially toxic metals. Ecological and geochemical studies were carried out in an area contaminated with waste from a disused Zn-Pb ore-washing plant. Between 1999 and 2019, the transformation of grassland and meadow vegetation into scrub and forest–grassland communities was observed. This transformation led to a decrease in the area of Molinietum caeruleae meadow (from 25.8% in 1999 to 10.7% in 2019), whose place was taken by Prunus spinosa and Rhamnus cathartica. The community of xerothermic limestone grasslands completely disappeared, being replaced in favour of the Diantho-Armerietum and Prunus spinosa community. In this period, the share of lifeforms of plants and species composition (46 and 60, respectively) also changed. The Shannon and Simpson biodiversity index reached high values in the second investigation period, and it was 0.893 and 0.86, respectively. The anthrosols had a high content of Zn—85,360 mg kg−1, Pb—28,300 mg kg−1, Cd—340 mg kg−1, and As—1200 mg kg−1. Carbonates, clay minerals, and fe-oxides are predominant in the mineral composition of the rhizosphere; the metal-bearing phases are stable; and hardly soluble minerals include smithsonite, cerussite, monheimite, hemimorphite, and oxides of Fe and Fe-Mn. Mineralisation/crust processes formed on the epidermis, and their influences on root development were found. Scanning electron microscopy and energy-dispersive X-ray spectroscopy studies on rhizosphere soil components provide information on the type of minerals and their susceptibility to heavy metals release. The identification of some biotic and mineral structures in rhizospheres can be an interesting source of information on pedogenic processes identified in back-scattered electron images.