The simplest means of altering the chemistry and electronic structure of any material, from molecular clusters to single crystals, is by the introduction of chemical impurities. We present a systematic study of the cation exchange reaction involving Co(2+) ions with metal benzenethiolate clusters, [M4(SPh)10](2-) (M = Zn, Cd), yielding diluted magnetic clusters having the general formula [(M1-xCox)4(SPh)10](2-). This method allows high concentrations of doping at the molecular level without forming concentrated magnetic clusters such as [Co4(SPh)10](2-). Changes in the electronic structure of the molecular species containing on average <1 Co(2+) per cluster were observed and characterized by a variety of analytical (high-resolution electrospray mass spectrometry) and spectroscopic techniques (electronic absorption including stopped-flow kinetics, luminescence, and paramagnetic (1)H NMR). The mass spectrometry results strongly suggest that the cation exchange reaction with Co(2+) is thermodynamically favored for the [Zn4(SPh)10](2-) cluster compared to the [Cd4(SPh)10](2-) clusters at room temperature. The rate of the cation exchange is orders of magnitude faster for the [Cd4(SPh)10](2-) cluster than for [Zn4(SPh)10](2-) and is governed by ligand interconversion processes. This simple room temperature cation exchange into molecular clusters is a model reaction that provides important structural information regarding the effect of Co(2+) doping on the cluster stability.