Highly luminescent CdSe and CdTe quantum dots (QDs) are prepared in a hot solvent of capping molecules (TOP/TOPO/HDA for CdSe and TOP/DDA for CdTe). The influence of exchange of the capping molecules with different types of thiol molecules (amino ethanethiol, (3-mercaptopropyl)trimethoxysilane, hexanethiol, 2-propenethiol, and 4-mercaptophenol) is investigated for both CdSe and CdTe QDs. A remarkable difference is observed: capping exchange with thiol molecules results in an increased luminescence efficiency for CdTe QDs but induces quenching of the excitonic emission of CdSe QDs. The striking difference between the two types of II-VI QDs is explained by the difference in the energy of the valence band top. The lower energetic position of the valence band for CdSe results in hole trapping of the photogenerated hole on the thiol molecule, thus quenching the luminescence. For CdTe the valence band is situated at higher energies with respect to the redox level of most thiols, thus inhibiting hole trapping and maintaining a high luminescence efficiency.