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Plant–soil interactions of endangered species with a high-priority conservation status are important to define in situ and ex situ conservation and restoration projects. The threatened endemic Coincya transtagana, thriving in the southwest of the Iberian Peninsula, can grow in metalliferous soils. The main goal of this study was to investigate the behavior of this species in soils rich in potentially toxic elements in the abandoned Aparis Cu mine. Soil samples were characterized for physicochemical properties and multielemental composition, as well as biological activity, through an analysis of enzymatic activities. Plant biomass was assessed, and multielemental analysis of the plants was also performed. The mine soils had slightly basic pH values and were non-saline and poor in mineral N-NH4, with medium-to-high organic matter concentration and medium cation-exchange capacity. In these soils, dehydrogenase had the highest activity, whereas protease had the lowest activity. The total concentrations of Cu (1.3–5.9 g/kg) and As (37.9–118 mg/kg) in soils were very high, and the available fraction of Cu in the soil also had high concentration values (49–491 mg/kg). Moreover, this study shows for the first time that C. transtagana had high uptake and translocation capacities from roots to shoots for Cu, Ni, and Cr. Although Cu in the plants’ aerial parts (40–286 mg/kg) was considered excessive/toxic, no signs of plant toxicity disorders or P uptake reduction were detected. This preliminary study revealed that C. transtagana is Cu-tolerant, and it could be used for phytoremediation of soils contaminated with potentially toxic elements, while also contributing to its conservation.