Large scale Molecular Dynamics simulations have been performed in order to study the response under mechanical deformation of pristine silica glass and its disordered structure, analogous to the one obtained after the initiation of displacement cascades. Results of the nanoindentation simulations show the extent of sink-in and the fact that hardness, calculated using two different methods yields similar values for the two glasses. Afterwards, the extent of the process zone was defined and the densification below the indentation mark was quantified. It was found that the pristine glass exhibits a slightly larger densification while the densified areas for both glasses were found to have a form which is similar to the one reported in recent experiments. The analysis of microstructural characteristics demonstrated an increase in the number of highly coordinated atoms inside the process zone during the loading phase, followed by a partial reversal during unloading. The calculation of the ring distributions for the two structures showed that at the time of loading there is an increase in the number of small rings and a simultaneous decrease of larger ones. During unloading, the reversal in the case of the disordered glass is more pronounced, indicating a better elastic recovery. The examination of the angular distributions and Si O bond orientation during the course of the nanoindentation simulations implies that deformation of the glass matrix occurs via distortion of the SiO 4 tetrahedral units, alongside a slight rotation, while probing the Si O bonds indicated the absence of significant plastic flow. Finally, a short discussion on the effect that relaxation time and other simulation parameters can have on the hardness results is made, alongside propositions for future work. • Large-scale Molecular Dynamics nanoindentation simulations were performed. • The systems under study were pristine and disordered silica glass. • Relaxation effects can be important for the estimation of hardness. • Increase of small rings and decrease of larger ones during loading • Densification is the primary means of deformation, alongside tetrahedral rotation.