Luminescence spectroscopy measurements of ZnSe/GaAs(100) heterojunctionsgrown by molecular beam epitaxy reveal the formation of deep levels near ‘‘buried’’ interfaces upon thermal annealing. A pronounced emission at 1.9–2.0 eV appears at temperatures in the 300–400 °C range depending on the ZnSe growth conditions with a constant activation energy of 1.10 eV. X‐ray photoemission spectroscopy indicates a correlation between this deep level and atomic diffusion of Ga and Zn across the heterointerface. Zn‐rich ZnSe growth conditions dramatically reduce this emission, highlighting the importance of local interface composition on thermal stability.