Biosynthesized gold nanoparticles (GNPs) were transferred from water to a hydrophobic ionic liquid (IL), [Bmim]PF6, with the assistance of alkyl trimethyl ammonium bromide. The phase transfer mechanism was illustrated through the exemplification of cetyltrimethyl ammonium bromide (CTAB). Interaction between GNPs and CTAB was demonstrated through zeta potential analysis. Moreover, an anion-exchange process was discovered between CTAB and IL. During the process, the hydrophobic CTAPF(6) formed in situ on the GNPs led to the hydrophobization and thus phase transfer of the GNPs. The phase transfer efficiency was found to be size-dependent.