Developing new rare-earth-doped optical glasses with "enhanced" spectroscopic properties requires the elaboration of new glass compositions. To overcome some typical limitations of silica glass, a strategy consists in encapsulating rare-earth (RE) ions within oxide nanoparticles (NPs) through a phase separation mechanism. In this paper, Molecular Dynamics simulations were performed using an interatomic potential reproducing the phase separation within a MgO–SiO2 binary melt to obtain RE-codoped glass models with RE = Eu or Er. In these structures, we observed that Mg-rich regions, included into a silica-rich matrix and identified as NPs, are amorphous and exhibit a large range of sizes. We showed that such nanoparticles are the host of a depolymerization phenomenon of the NPs’ SiO4 tetrahedral network leading to a release of non-bridging oxygen atoms. In the NPs, the MgO concentration increases and the doping RE ions are mainly located into the NPs where they are over-concentrated compared with the nominal doping concentration. However, the induced clustering effect is limited because of the non-bridging-oxygen-rich environment encountered in the NPs. This numerical analysis allows to give an insight on the chemical composition of the NPs, and especially on the local environment of the encapsulated rare-earth ions.