Despite the frequent use of silver nanoparticles (Ag NPs) embedded in materials for medical or optical applications, the effect of the matrix on the nanoparticle properties remains largely unknown. This study aims to shed light on the effect of an amorphous silica matrix on the structure and charge distribution of 55- and 147-atom silver nanoparticles by means of dispersion-corrected DFT calculations. Particular attention is paid to nanoparticle size and concentration effects and to the impact of the presence of native defects in the matrix. Covalent bonding between the silver nanoparticles and the matrix is found to occur at the interface. Such interface reconstruction involves the breaking of Si-O bonds, which systematically leads to the formation of Ag-Si bonds, and in some cases, to the formation of Ag-O ones. Interestingly, these interface reconstructions are accompanied by electron depletion of the nanoparticles, a substantial number of electrons being transferred from the two outer shells of the Ag NPs to the surrounding silica medium. The electrons lost by the nanoparticles are captured by the Si atoms involved in the interface bonds, but also, unexpectedly, by the undercoordinated silica defects that act as electron pumps and by the atoms of the silica network inside a few angströms spherical shell around the silver nanoparticle. The numbers of interface bonds and electrons transferred to the surrounding silica shell appear to be proportional to the surface area of the Ag NP. The electronic extension within silica goes beyond that attributable to the Ag NP spill-out. The presence of additional electrons in the matrix, especially on defects, is consistent with the experimental literature.