Fe–Mn–O magnetic nanocrystals precipitate in a glass system SiO2/Na2O/Fe2O3/MnO during thermal annealing for different periods of time. We report here small angle neutron scattering investigations using polarized neutrons (pSANS) on these glass samples. Analysis of scattering data reveals the formation of spherical core–shell particles. The core of the particle is found to be magnetic and it is surrounded by a non-magnetic shell-like region. The size parameters of the nanocrystals calculated by pSANS data analyses are comparable with the small angle X-ray scattering (SAXS) investigations, previously reported. Contrary to other glasses in the studied system the diffusion of Fe and Mn ions is not impaired by a rigid shell. This is explained by decreasing of the glass transition temperature of the shell region while its composition departs from that of the matrix.