Cd 1− x Mn x S nanocrystals (NCs) were successfully grown in a glass matrix and investigated by photoluminescence (PL), electron paramagnetic resonance (EPR) and magnetic force microscopy (MFM). We verified that the luminescent properties of these NCs can be controlled both by changing the x concentration and by thermal annealing of the samples. The EPR and PL data showed that the characteristic emission of Mn 2+ ions (4 T 1–6 A 1) is only observed when this magnetic impurity is substitutionally incorporated in the Cd 1− x Mn x S NC core (site S I). Besides, it was observed that the emission (4 T 1–6 A 1) suppression, caused by the Mn 2+ ion presence near the surface (site S II) of the Cd 1− x Mn x S NCs, is independent of the host material. The MFM images also confirmed the high quality of the Cd 1− x Mn x S NC samples, showing a uniform distribution of total magnetic moments in the nanoparticles.