Scanning tunneling microscopy (STM) and spectroscopy (STS) in combination with density functional theory (DFT) calculations are employed to study the surface and subsurface properties of the metastable phase of the phase-change material Ge 2 Sb 2 Te 5 as grown by molecular beam epitaxy. The (111) surface is covered by an intact Te layer, which nevertheless permits the detection of the more disordered subsurface layer made of Ge and Sb atoms. Centrally, we find that the subsurface layer is significantly more ordered than expected for metastable Ge 2 Sb 2 Te 5 . First, we show that vacancies are nearly absent within the subsurface layer. Secondly, the potential fluctuation, tracked by the spatial variation of the valence band onset, is significantly less than expected for a random distribution of atoms and vacancies in the subsurface layer. The strength of the fluctuation is compatible with the potential distribution of charged acceptors without being influenced by other types of defects. Thirdly, DFT calculations predict a partially tetrahedral Ge bonding within a disordered subsurface layer, exhibiting a clear fingerprint in the local density of states as a peak close to the conduction band onset. This peak is absent in the STS data implying the absence of tetrahedral Ge, which is likely due to the missing vacancies required for structural relaxation around the shorter tetrahedral Ge bonds. Finally, isolated defect configurations with a low density of 10 −4 nm −2 are identified by comparison of STM and DFT data, which corroborates the significantly improved order in the epitaxial films driven by the buildup of vacancy layers.