In this investigation, glasses from the system Na2O/MnO/SiO 2/Fe2O3 are prepared using a conventional glass-melting technique. During annealing the glass, a nanocrystalline (Fe, Mn)-based spinel phase is precipitated. The phase composition and microstructure of the formed glass-ceramics are studied using X-ray diffraction and electron microscopy. Anomalous small-angle X-ray scattering experiment is used to gather information on the size, composition and element distribution for the precipitated (Fe, Mn)-based nanocrystals. The sizes of the formed spinel crystals, as determined by scanning electron microscopy and anomalous X-ray scattering, are in the range from 12 to 50 nm for annealing temperatures in the range from 550 to 700 °C. Annealing for a longer period of time at temperatures ≥600 °C results in the formation of a second crystalline phase, NaFe(SiO3)2 (aegirine). The ASAXS data show the formation of core-shell structure for the (Fe, Mn)-based crystals with core consisting mostly of iron oxide and a shell, depleted of Fe and Mn. The growth of the spinel crystals is assumed to be kinetically self-constrained.