We investigate the effect of co-implanting a silicon sublayer on the thermal diffusion of germanium ions implanted into SiO2 and the growth of Ge nanocrystals (Ge-ncs). High-resolution imaging obtained by transmission electron microscopy and energy dispersive spectroscopy measurements supported by Monte-Carlo calculations shows that the Si-enriched region acts as a diffusion barrier for Ge atoms. This barrier prevents Ge outgassing during thermal annealing at 1100 °C. Both the localization and the reduced size of Ge-ncs formed within the sample region co-implanted with Si are observed, as well as the nucleation of mixed Ge/Si nanocrystals containing structural point defects and stacking faults. Although it was found that the Si co-implantation affects the crystallinity of the formed Ge-ncs, this technique can be implemented to produce size-selective and depth-ordered nanostructured systems by controlling the spatial distribution of diffusing Ge. We illustrate this feature for Ge-ncs embedded within a single SiO2 monolayer, whose diameters were gradually increased from 1 nm to 5 nm over a depth of 100 nm.