Many efforts have been undertaken in past decades to minimize pollution from municipal solid waste incineration fly ash (MSWI FA). This residue is toxic, because of its high concentration of heavy metals, mainly Pb and Zn. A new method for heavy metals entrapment with MSWI FA was proposed recently. The method is based on the use of colloidal silica and it was applied to other FA typologies (flue gas desulfurization and coal fly ashes). The first results, in terms of material recovery, are very promising. The present paper is dedicated to the study of the mechanism of entrapment of heavy metals as promoted by the use of colloidal silica in the inertisation process by means of X-ray Absorption Spectroscopy (XAS) and by synchrotron-based XRD. Only XAS allowed focussing on the local environmental changes for Pb and Zn atoms on a molecular level. Chemical equilibrium calculations predict that, without silica, water-soluble Pb and Zn salts form stable phases, such as carbonates. XAS analysis showed that, despite carbonation of alkaline earth metals such as Ca, colloidal silica promotes the stabilisation of major heavy metals in phases other than carbonates and most likely in the more inert silicate form.