This scientific paper describes the chemical study of different Al2O3/GaN interfaces found in the new generation of high electron mobility transistors developed for power electronics applications. The stake for these interfaces is the limitation, ideally the absence of an oxidized gallium layer hampering the good electrical behavior of the semiconductor. These structures have been studied through time-of-flight secondary ion mass spectrometry (ToF-SIMS), magnetic SIMS (M-SIMS), and atomic force microscopy (AFM) analyses. Two structures were considered: a bilayer Al2O3 10 nm–GaOx 2 nm on GaN and a Al2O3 10 nm single layer deposited on preliminary etched GaN. The first sample was used as a dedicated reference sample where an actual gallium oxide layer was grown, whereas the second one was a technologically relevant structure. Several experimental conditions were compared for the ToF- and M-SIMS analyses; in particular, three angles of incidence for the primary Cs+ sputter beam (65°, 61°, 45°) were used, leading to diverse depth resolutions and roughnesses, as revealed by surface topography analysis provided by AFM. Among the different incidence angles, it was found that the best experimental conditions were those obtained by ToF-SIMS analysis with an incidence angle of 45°, generating the least roughness.