Replacement of protecting ligands of gold nanoclusters by ligand exchange has become an established post-synthetic tool for selectively modifying the nanoclusters' properties. Several Au nanoclusters are known to additionally undergo size transformations upon ligand exchange, enabling access to cluster structures that are difficult to obtain by direct synthesis. This work reports on the selective size transformation of Au15(SG)13 (SG: glutathione) nanoclusters to Au16(2-PET)14 (2-PET: 2-phenylethanethiol) nanoclusters through a two-phase ligand exchange process at room temperature. Among several parameters evaluated, the addition of a large excess of exchange thiol (2-PET) to the organic phase was identified as the key factor for the structure conversion. After exchange, the nature of the clusters was determined by UV-vis, electrospray ionization-time of flight mass spectrometry, attenuated total reflection-Fourier transform infrared, and extended x-ray absorption fine-structure spectroscopy. The obtained Au16(2-PET)14 clusters proved to be exceptionally stable in solution, showing only slightly diminished UV-vis absorption features after 3 days, even when exposed to an excess of thiol ligands.