Dietary deficiencies of zinc and iron are a substantial global public health problem. An estimated two billion people suffer these deficiencies(1), causing a loss of 63 million life-years annually(2,3). Most of these people depend on C-3 grains and legumes as their primary dietary source of zinc and iron. Here we report that C-3 grains and legumes have lower concentrations of zinc and iron when grown under field conditions at the elevated atmospheric CO2 concentration predicted for the middle of this century. C-3 crops other than legumes also have lower concentrations of protein, whereas C-4 crops seem to be less affected. Differences between cultivars of a single crop suggest that breeding for decreased sensitivity to atmospheric CO2 concentration could partly address these new challenges to global health.