The direct synthesis of zeolites in polluted soils has proved to be a promising process for the stabilization of metals inside these minerals. Nevertheless, more detailed information about this process is still needed in order to better foresee the fate of metals in treated soils. In this work, zeolite X has been synthesized under alkaline conditions in an aqueous solution containing 2500 mg kg −1 of Cu, starting from Na silicate and Al hydroxide at 60 °C. Aluminium, Si and Cu concentrations in the aqueous phase, during zeolite synthesis, were measured over a period of 160 h. The solid products have been characterized over time by XRD, SEM-EDX, ESR, FT-IR, and synchrotron radiation X-ray microbeam absorption near edge structure (μ-XANES) and extended X-ray absorption fine structure (μ-EXAFS) spectroscopy. It appears that the marked reduction of Cu concentration in solution is not only due to a simple precipitation effect, but also to processes connected with the formation of zeolite X which could entrap, inside its porous structure, nano- or micro-occlusions of precipitated Cu hydroxides and/or oxides. In addition, EXAFS observations strengthen the hypothesis of the presence of different Cu phases even at a short-range molecular level and suggest that some of these occlusions could be even bound to the zeolite framework. The results suggest that zeolite formation could be used to reduce the availability of metals in polluted soils.