Climate change and rising carbon dioxide (CO2) levels are expected to reduce the mineral nutrient content of soybean seeds. The main objective of this study was to survey diverse soybean germplasm for variation in seed elemental concentrations and their relationships between elements, protein content, and individual seed weight. Seeds from 90 soybean genotypes were weighed and subjected to inductively coupled plasma-mass spectrometry (ICP-MS) ionomics analysis and Carbon/Nitrogen (C/N) analysis to determine protein. The results demonstrated substantial variation with the possibility of significantly improving most mineral nutrients, especially selenium (Se), copper (Cu), iron (Fe), and manganese (Mn). This diverse survey identifies genotypes that can complement existing soybean breeding programs for improving seed nutritional quality. Correlation analysis identified two clusters of co-variant elements: zinc (Zn), phosphorus (P), and sulfur (S) as well as Zn, Cu, Se, and rubidium (Rb) were positively correlated with each other. Tolerable upper limits of Rb intake are not defined for humans illustrating the need to monitor trace elements along with desirable nutrients.