The incorporation of substitutional Co2+ impurities in [Cd10S4(SPh)16]4– (Cd10) molecular clusters prepared by the self-assembly method where Na2S is the sulfur precursor and a redox method where elemental S is the sulfur precursor is studied. The Co2+ ions provide unique spectroscopic and chemical handles to monitor dopant speciation during cluster formation and determine what role, if any, other cluster species play during Cd10 cluster formation. In contrast to the redox method that produces exclusively surface-exchanged Co2+-doped Cd10 (Co:Cd10), the preparation of Cd10 by the self-assembly method in the presence of Co2+ ions results in Co2+ incorporation at both the surface and core sites of the Cd10 cluster. Electrospray ionization mass spectrometry (ESI–MS) analysis of the dopant distribution for the self-assembly synthesis of Co:Cd10 is consistent with a near-Poissonian distribution for all nominal dopant concentrations albeit with reduced actual Co2+ incorporation. At a nominal Co2+ concentration of 50%, we observe incorporation of up to seven Co2+ ions within the Cd10 self-assembled cluster compared to a maximum of only four Co2+ dopants in the Cd10 redox clusters. The observation of up to seven Co2+ dopants must involve substitution of at least three core sites within the Cd10 cluster. Electronic absorption spectra of the Co2+ ligand field transition in the heavily doped Co:Cd10 clusters display clear deviation with the surface-doped Co2+-doped Cd10 clusters prepared by the redox method. We hypothesize that the coordination of Co2+ and S2– ions in solution prior to cluster formation, which is possible only with the self-assembly method, is critical to the doping of Co2+ ions within the Cd10 cores.