Water-soluble doped quantum dots have unique photophysical properties and functionalities as optical labels for bioimaging and chemo-/biosensing. However, doping in quantum dots is not easy due to the dopant-ion size mismatch and "self-purification" effect. Here, we demonstrate a successful preparation of Mn-, Cu-, and Ni-doped CdS quantum dots with bimetallic clusters instead of ions as building blocks under mild aqueous conditions up to gram scale. The representative Mn-doped quantum dots have uniform size, about 3.2 ± 0.5 nm, and emit at 620 nm. The doping concentration can be adjusted in the range 6.4%-25.7%. On the premise of good water solubility, they are stable and nontoxic so as to be directly used for cell imaging. Copper and nickel doping have similar results. Because of the close sizes of bimetallic clusters and the low reaction temperature, the challenges posed by dopant size mismatch and ion diffusion are ignored. X-ray absorption fine structure analysis proves that dopants are inside the quantum dots rather than on the surface, indicating that the "self-purification" effect can be effectively overcome. Furthermore, codoped ZnS quantum dots with adjustable emission are achieved, which validates the versatility of our new approach.