The fabrication of Si nanocrystals (NCs) in multilayer structures based on HfO2 and alloys for memory applications is carried out using an innovative method, the ultra-low energy (1 keV) ion implantation followed by a post-implantation annealing. Si+ ions are implanted into SiO2 thin layers deposited on top of thin HfO2-based layers. After annealing at high temperature (1050°C), the implantation leads to the formation of a two dimensional array of Si NCs at a distance from the surface larger than expected, due to an anomalous oxidation of the implanted Si. Nevertheless, the best memory windows are obtained at lower thermal budget, when no nanocrystals are present in the layer. This suggests that electrical measurements should always be correlated to structural characterization in order to understand where charge storage occurs.