We report a simple surface functionalization of glutathione-capped gold nanoclusters by hydrophobic ion pairing with alkylamine followed by a complete phase transfer to various organic solvents with maintained colloidal stability and photoluminescence properties. The described surface hydrophobication enables efficient encapsulation of gold nanoclusters into PLGA nanocarriers allowing their visualization inside cultured cells using confocal fluorescent microscopy. The simplicity and efficiency of the described protocols should extend the biomedical applications of these metallic nanoclusters as a fluorescent platform to label hydrophobic polymeric nanocarriers beyond conventional organic dyes.