We demonstrated the possibility of acquiring Raman spectra of colloidal quantum dots (QDs) at low concentration in water with a size as small as 2.5 nm in diameter using Raman tweezers microspectroscopy. We measured the spectra of CdSe QDs capped with thioglycerol and with L-cysteine. This technique was applied to probe the interaction between Co 2+ and Cys-CdSe QDs whose fluorescence emission is quenched in the presence of this metal cation. The quenching mechanism was so far hypothetical. The Raman spectra of Cys-CdSe QDs recorded in the absence and in the presence of Co 2+ demonstrated the binding of Co 2+ cations to the carboxylate groups of the L-cysteine ligand grafted on the surface of the 4.2 nm CdSe QDs. The frequency of modes for the grafted ligand is changed with respect to the free ligand in solution. Considering the vibrational coupling between the excitonic state and the ligand, we inferred that the binding of a metal cation to the grafted ligand modifies this coupling, so that exciton relaxation through crystal defects is favored. This result rationalizes the fluorescence quenching observed during the metal cation-QD interaction.