The stability of embedded Indium (In) nanoclusters (NCs) in silica under thermal annealing and ion irradiation was investigated. The In NCs were prepared by implantation of 890 keV indium ions in silica matrix at room temperature. Post implantation annealing resulted in the shifting of the size distribution to higher side. On the other hand 140 keV Nitrogen ion irradiation at elevated temperature resulted in the reduction of NCs size, with significant narrowing of the size distribution. The paper discusses the results of the study in the light of the models pertaining to the stability of NCs under ion irradiation conditions.