Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with canopy position. Seeds produced at the top of the canopy have higher concentrations of protein but less oil and minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Altering the microenvironment within the soybean canopy affected the gradients in protein and oil without altering the distribution of Mg, Fe and Cu, suggesting different underlying mechanisms. Metabolomic analysis of developing seeds suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds. Our results establish a new category of seed heteromorphism and provide an unexpected approach to link agronomic practices to improve human nutrition and health by using seeds produced in the lower canopy for production of iron-rich soy foods for human consumption.