In the context of developing new soil remediation technologies, zeolites can be directly synthesised in soil from fused coal fly ash to reduce heavy metals mobility and availability. Such a process promotes the formation of metal hydroxide/oxide precipitates which can also form occlusions inside the structure of the forming minerals. The proposed method has been studied in an agricultural soil artificially polluted by high amounts of Cu or Cd (15 mg of metal/g of soil dry weight) and treated with fused coal fly ash (1:10 w/w) at 30 and 60°C. The process has been monitored for a period of one year after fly ash application to soil. During the observation period different types of zeolites have been formed: zeolite X, zeolite P, and zeolite A. The crystallized zeolites have been characterized for their abundance, structure, chemical composition and size by means of quantitative X-Ray Diffraction (XRD) and an automated single particle analysis method using Electron Probe X-ray Microanalysis (EPXMA). During zeolite synthesis, a concomitant strong reduction in Cu and Cd mobility (as evidenced by a marked increase in the Kd value) was observed. In addition, a reduction in Cu and Cd availability has been observed during zeolite synthesis by sequential extractions with EDTA (5 mM, pH 7.5). This approach allowed for an estimation of the percentage of the metal effectively stabilised in the solid phase at the end of the observation period varying from 20 to 40%. Synchrotron radiation based X-ray microanalytical techniques such as micro X-ray Fluorescence (µ-XRF) tomography and µ-XRD allowed for the visualisation of the entrapment of heavy metal clusters inside the zeolitic structures. By using different spectroscopic techniques such as Electron Spin Resonance (ESR), Fourier-Transformed Infra-Red (FT-IR) spectroscopy, and micro X-ray Absorption Fine Structure Spectroscopy (µ-XAFS) it was possible to define the nature of the metal clusters inside zeolites mainly as hydroxides/oxides even partly bound to the zeolite framework. The presence and nature of metal precipitates occlusions inside the forming zeolite minerals may have also favoured the preferential synthesis of certain zeolitic structures over others. All the obtained information could be useful as basic knowledge for planning new technologies for the physicochemical stabilization of heavy metals in heavily polluted soils.