The ion beam synthesis of Pb nanoparticles (NPs) in silica is studied in terms of a two step thermal annealing process consisting of a low temperature long time aging treatment followed by a high temperature short time one. The samples are investigated by Rutherford backscattering spectrometry and transmission electron microscopy. The results obtained show that highly stable Pb trapping structures are formed during the aging treatment. These structures only dissociate at high temperatures, inhibiting the nucleation of NPs in the metallic phase and causing an atomic redistribution that renders the exclusive formation of a two dimensional, uniform and dense array of Pb NPs at the silica–silicon interface. The results are discussed on the basis of classic thermodynamic concepts.