Abstract Accurate assessment of soil contamination by potentially toxic elements requires knowledge of local background values; only in this way can false positives or negatives be avoided. The objective of this study was to define environmental background concentrations of potentially toxic elements in soils of the Yucatán Peninsula. Based on systematic sampling, 116 sites across the Yucatán Peninsula were selected for surface soil sampling (5–15 cm); additionally, total elemental content and mineral composition were analyzed in four soil and rock profiles, each representative of one of the four major lithological zones. Soil and rock samples were analyzed using portable X-ray fluorescence (XRF) and X-ray diffraction (XRD) equipment. Concentrations of Cr (382 mg/kg), Fe (62,302 mg/kg), Mn (2,124 mg/kg), Pb (50 mg/kg), and Zn (170 mg/kg) are proposed as local environmental background levels for soils in the Yucatán Peninsula. The results of the elemental and mineralogical analysis of soils and rocks confirmed that analyzing surface soil samples is a suitable approach for establishing environmental background levels. Based on the elements analyzed, three concentration ranges—local background level, investigation level, and mandatory investigation level—were proposed to support Mexican authorities in decision-making.