Samples composted of chemically synthesized Au nanoparticles (NPs) (16.0±2.0 nm) embedded within a planar silica film are used as model system to investigate the evolution of a second phase under irradiation when the temperature and the ion stopping power are changed. Samples are irradiated with 4 MeV Au2+ ions and 4 MeV Br2+ ions for temperature ranging from 30 °C up to 800 °C and for fluences up to 8×1016 cm−2. We show that at room temperature the complete dissolution of the NPs leads to the formation of smaller precipitates with a narrower size distribution, i.e., 2.0±0.3 nm. However, when the temperature is increased and/or the nuclear stopping power is decreased, a reduction in the dissolution rate was observed. This leads to the formation of a bimodal size distribution. Finally, the evolution of the density of the precipitates with the temperature is discussed in term of the thermal stability of the irradiation-induced defects within the silica matrix.