Au nanoparticles (NPs) with a size in the 2–12 nm range have been grown in silica by 2 MeV Au-ion implantation and a subsequent thermal annealing in air. The as-prepared Au NPs were irradiated with 10 MeV Si ions elongating some of them. From transmission electron microscopy in Z-contrast mode, we observed a narrow size distribution of the minor axis of the deformed NPs, which presents its higher frequency around 6–7 nm and have a saturation about 9 nm. This final result agrees well with the diameter of the track formed by Si ions of 10 MeV in silica, supporting the thermal spike model, which would explain the deformation of the NPs. In this model, the NP melts and creeps along the ion track. Our results show that the NP crystallization is in the fcc structure. On the other hand, a 200 keV electron irradiation provoked roundness on the previously elongated nanoparticles. This effect was observed in situ by high-resolution transmission electron microscopy, showing additionally that, during the roundness process, the fcc structure, as well as its crystalline orientation, remain unchanged. Thus, this study shows how Au NPs embedded in silica, within this size distribution, keep the fcc bulk structure under both ion and electron irradiations.