Au-silica core-shell nanoparticles have been irradiated with 20 keV He + ions up to a maximum fluence of 4.7 × 10 17 ions/cm 2. the nanoscale structural and crystallographic evolution induced by He + ion irradiation was followed at various stages using transmission electron Microscopy (teM). During irradiation satellite Au clusters are formed around the main Au core, which remained crystalline even after the maximum He + ion fluence. The spherical silica shell deformed into a hemisphere due to He + ion irradiation. three dimensional Monte-carlo simulations, based on the binary collision approximation, have been performed on stacked infinite layers and an individual particle. The stacked layers results show that the He + beam interacts with most of the nanoparticle and Au migrates in the direction of beam incidence agreeing with experimental findings. The individual particle results match the experiment in terms of the volume which is sputtered away however additional mechanisms, not included in the simulations, are present in the experiment during the satellite formation and silica shell deformation. These results show the ability for 20 keV He + ions to be used for the modification of nanostructures. furthermore, these results contribute to a quantitative understanding of the dynamic evolution of materials observed using microscopy techniques based on He + ions.