The regulation of photosynthesis through changes in light absorption, photochemistry, and carboxylation efficiency has been studied in plants grown in different environments. Iron deficiency was induced in sugar beet (Beta vulgaris L.) by growing plants hydroponically in controlled growth chambers in the absence of Fe in the nutrient solution. Pear (Pyrus communis L.) and peach (Prunus persica L. Batsch) trees were grown in field conditions on calcareous soils, in orchards with Fe deficiency-chlorosis. Gas exchange parameters were measured in situ with actual ambient conditions. Iron deficiency decreased photosynthetic and transpiration rates, instantaneous transpiration efficiencies and stomatal conductances, and increased sub-stomatal CO2 concentrations in the three species investigated. Photosynthesis versus CO2 sub-stomatal concentration response curves and chlorophyll fluorescence quenching analysis revealed a non-stomatal limitation of photosynthetic rates under Fe deficiency in the three species investigated. Light absorption, photosystem II, and Rubisco carboxylation efficiencies were down-regulated in response to Fe deficiency in a coordinated manner, optimizing the use of the remaining photosynthetic pigments, electron transport carriers, and Rubisco.