Anthropogenic activities contaminate the soils of millions of hectares worldwide with toxic elements. Native species, such as the Amazonian species Stryphnodendron pulcherrimum, can mitigate the effects of these elements in soil and have motivated research on phytoremediation. The study’s objective was to analyze the levels of inorganic components present in rhizosphere soil, roots, and leaves of S. pulcherrimum in two urban areas in the metropolitan region of Manaus, Brazil. Eight samples of soil, leaves, and roots of S. pulcherrimum were collected in different areas, totaling 48 samples, using X-rays by total reflection to quantify trace elements present. Graphical dispersion was performed using the Principal Component Analysis Method (PCA). The anthropic area provided the predominance of elements such as Y, Sc, Nb, and Hf, and the forest fragment showed high concentrations of Cu, Yb, and Ba. Our results indicate that S. pulcherrimum is a species with the potential for phytoremediation in areas with the presence of heavy metals in soil. The species in the forest fragment presented high leaf concentrations of Cr, Y, and Yb, suggesting that it may be used for biomonitoring soils. This is the first report of this species as a bioaccumulator of heavy metals.