AlGaN-based quantum well (QW) heterostructures grown by plasma-assisted molecular beam epitaxy on c-Al2O3 substrates have been studied. The high-temperature (785 °C) synthesis of AlN buffer layer nucleated by a migration-enhanced epitaxy and including several ultrathin GaN interlayers was the optimum approach for lowering the threading dislocations density down to 108–109 cm−2. High-angle annular dark-field scanning transmission electron microscopy (HAADF STEM) has revealed the step-like roughness of the AlN/Al2O3 interface. Also, the formation of Al-rich barriers induced by temperature-modulated epitaxy and the spontaneous compositional disordering have been found in the Al
N (x > 0.6) barrier layers. The origin of these phenomena and their influence on parameters of the mid-UV stimulated emission observed in the QW heterostructures were discussed. The fine structure of the QWs formed by a submonolayer digital alloying technique has been displayed by HAADF STEM, and optical properties of the QW structures were studied by temperature- and time-dependent photoluminescence spectroscopy.