Silicon (Si) is a beneficial element for plants as it increases their resistance to several biotic and abiotic stresses. In the rhizosphere, root exudates, especially when released by nutritionally stressed plants, promote the mineral weathering and, consequently, influence Si biogeochemistry. This study aims at evaluating the mineralogical alterations in the rhizosphere of Fe-deficient or Fe-sufficient barley plants grown either in a natural or in an artificial calcareous soil, focusing on the dynamics of both Fe and Si. After 6 d of soil-plant contact, X-ray diffraction (XRD) analysis of rhizosphere soil samples of Fe-deficient plants revealed, for both natural and artificial soil, a decrease of amorphous phases and an increase of smectite compared to the unplanted soil. Root exudates released by Fe-deficient plants were most likely the main responsible for the weathering of the amorphous phases by a ligand controlled dissolution mechanism. When the soil-plant contact was prolonged up to 12 d, plants overcame Fe nutritional stress and their effect on soil mineralogy completely changed, as proved by the considerable increase of amorphous and decrease of smectite. Smectite decrease might evidence the effort of plant to mobilize Si and micronutrients other than Fe from the soil through the exudation of organic ligands. When the artificial soil was treated with Fe-sufficient barley plants, the mineral weathering trend appeared reversed compared to the experiments with Fe-deficient plants. Plant nutritional status regulates the root exudation pattern and, consequently, drives mineral weathering processes in the rhizosphere. Barley has shown to be able to mobilize Si from smectite, yet depending on its Fe supply and proving the strict connection between Si and Fe dynamics in the rhizosphere.