The impact of device processing and plasma treatments at different plasma conditions on the electronic transport properties of GaN/AlGaN/GaN heterostructures was investigated as well as annealing in nitrogen atmosphere at 425°C. The electrical properties are characterized by Hall-effect measurements while electron spectroscopy and X-ray measurements are used to investigate changes in the surface chemical composition and in the layer structure, respectively. It is demonstrated that these layer structures are quite sensitive even to non-plasma based processing. Furthermore, treatments in SF6 and N2 based plasmas strongly affect the 2DEG properties of the heterostructure due to altering of the surface barrier accompanied by thinning of the layer structure. Depending on the layer structure and the plasma conditions used the electronic properties may be recovered by annealing.