The effect of short-chain alcohols and acetonitrile on the ligand shell composition and the photoluminescence quantum yield of purified PbSe and CdSe quantum dots is analyzed by solution NMR and photoluminescence spectroscopy. We find that short-chain alcohols induce the release of X-type carboxylate ligands with a concurrent reduction of the photoluminescence quantum yield, while acetonitrile does not. We interpret this difference in terms of the protic or aprotic character of both nonsolvents, where only the protic alcohols can provide the protons needed to desorb carboxylate ligands. We find similar differences between short-chain alcohols and acetonitrile when used as nonsolvents during the purification of crude synthesis products, a result stressing the importance of using aprotic nonsolvents for nanocrystal purification or processing.