Silicon is considered an important element in several crops because it improves growth and mitigates biotic and abiotic stress. In this work, the role of silicon in limiting Fe deficiency responses by improving photosynthesis and composition of thylakoid multiprotein complexes (MPCs) has been studied. Two-week-old soybean (Glycine max L.) plants grown hydroponically with a Fe-deficient solution without FeIII-EDTA were fed with 1.0 mM silicon in the form of sodium silicate [Na2SiO3]. Responses to four Si and Fe combined treatments were analyzed after 3 and 5 days. Leaf chlorosis was generated under Fe deficiency, with decreased chlorophyll and carotenoid contents. The negative effects observed were more severe under a prolonged period of Fe deficiency. Biomass and Fe concentration in roots and shoots were largely improved by Si supply under Fe deficiency. The rates of net photosynthesis, transpiration and stomatal conductance were highly improved by the supply of Si under Fe deficiency. MPCs proteins (thylakoid complex proteins) evaluated by the first dimension followed by second-dimensional 2D-BN-SDS-PAGE and MALDI–TOF/TOF–MS observation showed that the Fe deficiency greatly decreased thylakoid MPCs and also resulted in a closure of stomata. However, these impacts of Fe deficiency were largely restored in the presence of silicon. The observed responses to silicon supply in Fe-deficient plants indicate that silicon has a significant role in limiting Fe deficiency responses by improving photosynthesis and composition of thylakoid protein complexes. © 2015, Springer Science+Business Media New York.