Background and Aims: Soybean (Glycine max (L.) Merrill) stands out as the major source of protein and oil for human and animal nutrition. Nevertheless, the increase in soybean yield has been accompanied by a reduction in its protein content in the last few decades. Since this might be influenced by the elemental composition of the seeds, we herein aimed at determining the profile of mineral nutrients and protein of 95 soybean varieties broadly cultivated in Brazil, the biggest soybean producer and exporter worldwide, to identify possible nutritional triggers for the protein content. Methods: Energy dispersive fluorescence spectroscopy (EDXRF) was employed to determine the concentration of macro, i.e., (K), phosphorus (P), sulphur (S), calcium (Ca), and micronutrients, i.e., iron (Fe), manganese (Mn), zinc (Zn), and copper (Cu). The protein content was evaluated in soybean seeds by the Dumas method. The correlational and clustering assessment between nutrients and protein were determined through both univariate and multivariate non-parametric tests. Results: Both protein and nutrient concentrations are not homogeneous across soybean seed varieties, and a clear positive association between protein and sulphur (S), zinc (Zn), and manganese (Mn) concentrations were observed. Conclusion: The recorded results suggest that sulphur (S), zinc (Zn), and manganese (Mn) are the limiting nutrients for higher protein content in soybean seeds.