The State of Mato Grosso, Brazil, presents a great diversity of soils and landscapes, and many areas of agriculture and mining. However, the natural content of trace elements in the soil are still little known, which represents a great gap for studies and/or regulations concerning soil and food security. This study proposes to establishing quality reference values (QRVs) for trace elements in Mato Grosso soils. Soil sampling was carried out to cover the geodiversity of soils in this region, considering geology, geomorphology, lithology, pedology and biomes, in addition to summarizing the data available in the literature to form the database for this study. The soil was analyzed for the contents of Fe, Mn, Cu, Zn, Ni, Cr, Ba, Pb, As, Cd and Hg, according to the USEPA 3051A methodology. Trace element results based on soil geodiversity contributed to a general description of how levels of these elements may be related to the environmental factors studied. The levels of main elements related to the environmental factors were Mn and Zn to geology; Mn, Cr, Ba, Zn, As and Cd to geomorphology; Mn to lithology; Mn and Cr to pedology; and Mn, As, Cd and Hg to the biome. It was not possible to propose QRVs grouped by environmental factors for the State of Mato Grosso, especially due to the large territorial extension covered. Thus, the QRVs were proposed in the 90th percentile, in mg kg−1, as follows: Fe 23,128; Mn 351; Cu 16.50; Zn 29.24; Ni 8.86; Cr 52.73; Ba 84.45; Pb 13.42; As 7.60; Cd 0.87; and Hg 0.10. Mercury, Cd, and As levels require careful regional monitoring, as some environments, such as the Amazon biome, may present naturally high levels, and small alterations in the bioavailability of such elements might represent a risk to health or the environment.