Long-term agricultural sustainability is dependent in part on our capacity to provide productive, nutritious crops that minimize the negative impacts of agriculture on the landscape. Perennial grains within an agroforestry context offers one solution: These plants produce large root systems that reduce soil erosion and simultaneously have the potential to produce nutrients to combat malnutrition. However, nutrient compositions of wild, perennial, herbaceous species, such as those related to the common bean (Phaseolus vulgaris) are not well known. In this study, seed ion and amino acid concentrations of perennial and annual Phaseolus species were quantified using ionomics and mass spectrometry. No statistical difference was observed for Zn, toxic ions (e.g., As) or essential amino acid concentrations (except threonine) between perennial and annual Phaseolus species. However, differences were observed for some nutritionally important ions. For example, Ca, Cu, Fe, Mg, Mn, and P concentrations were higher in annual species; further, ion and amino acid concentrations appear to be largely independent of each other. These results suggest variability in ion and amino acid concentrations exist in Phaseolus. As new crop candidates are considered for ecological services, nutritional quality should be optimized to maximize nutrient output of sustainable food crops.