The field of semiconductor nanocrystals (NCs), known as quantum dots (QDs), has significantly advanced since their discovery in the early 1980s. Because the size distribution of typical NCs results in variations in their structure and properties, precisely controlling their size and shape has been a crucial challenge in nanochemistry. Early research on doping was primarily conducted on polydisperse NC hosts, whereas more recent studies, in pursuit of greater clarity, have shifted towards doping in monodisperse hosts, enabling more sophisticated interpretations of key aspects such as host structures, doping sites, and doping mechanisms. However, such studies on the mechanism of doping in colloidal nanocrystals remain limited. Considering the large surface-to-volume ratio of NCs, surface doping is more likely to occur than internal doping. Despite extensive efforts, the precise control of doping sites and a comprehensive understanding of the underlying doping mechanisms remain elusive. These ongoing challenges are further complicated by the ambiguous host structures of NCs and the difficulty of probing dopants and identifying their distinct locations. In this regard, Co2+ is a useful dopant due to spin-allowed ligand field (LF) transitions that occur in the visible region and produce a green color in tetrahedral coordination. The characteristic band shape and energy of the 4A2→4T1(P) transition is sensitive to the local Co2+ coordination environment, allowing dopant speciation to be determined. In this dissertation, Co2+ doping in atomically precise semiconductor clusters is investigated through two projects. The first study examines decameric cadmium chalcogenide clusters, (HNEt3)4[Cd10−xCoxE4(E'Ph)16] (E, E' = S, Se), which feature two distinct metal sites. To investigate how ligands affect Co2+ doping sites, we selected the four compositions of cadmium chalcogenide clusters as hosts. By identifying the dopant speciation in these clusters, we established the ligand preference of Co2+ as SPh− > μ3-S2− > SePh− > μ3-Se2−, which influenced the Co2+ substitution either at surface or core sites. The second study investigates Co2+-doped ZnS magic-size clusters (MSCs) synthesized from metal salts, polysulfide, and oleylamine. We found that at low temperatures (~130 °C), the cation exchange of Zn2+ with Co2+ resulted in exclusive surface Co2+ doping. However, at high temperatures (170-250 °C) the surface-doped Co2+:ZnS MSCs appear to undergo a coalescence process that gradually produces ZnS MSC with Co2+ at internal sites within the cluster.