Doped semiconductor nanocrystals (NCs) can address key problems in applications such as LED’s, photovoltaics, spintronics, and bioimaging, since doping enables further control over the properties of NCs. In this work, we report the successful doping of ZnSe NCs and ZnTe magic sized clusters (MSCs) with Mn2+ via cation exchange. The parent ZnTe MSCs consist of three cluster families with sizes 1.3, 1.5 and 1.8 nm. The parent ZnSe NCs have a diameter of 3 nm (<5% dispersion) and are highly luminescent. Mn2+ emission is observed for both doped materials, with a radiative decay time that is characteristic of Mn2+ in ZnTe and ZnSe, respectively. The absorption spectra of the NCs and MSCs remain virtually unchanged upon doping. Interestingly, the excitation spectra of the Mn2+ emission are characterized by the same absorption transitions observed for the undoped ZnSe NCs and ZnTe MSCs. This shows that the Mn2+ ions are excited through the exciton states of the host, providing further evidence that the emission originates from Mn2+ ions incorporated in the host, rather than simply bound to the surface. For some applications, like spintronics, very low doping concentrations are required. The approach developed here can be used to achieve low dopant concentrations, since doped MSCs can serve as nuclei for the growth of an undoped shell. Moreover, this strategy is very versatile, since the size and shape of the NCs is preserved after the cation exchange.