In this paper, the influence of a high-temperature (900 °C) selective oxidation process on the electrical properties of AlGaN/GaN heterostructures was investigated. In particular, electrical measurements performed on appropriate devices and test patterns demonstrated that the current flow through the two-dimensional electron gas (2DEG) was suppressed, even if the thickness of the local oxide did not reach the AlGaN/GaN interface. The combination of macroscopic current-voltage and capacitance-voltage measurements with depth-resolved scanning capacitance microscopy elucidated the doping dependence and the compositional stability of the material during high-temperature oxidation. The reduction in the 2DEG sheet carrier density and the variation of the threshold voltage of simple high electron mobility transistor structures upon high-temperature annealing were also discussed.