The electrical behaviour of graphene (Gr) contacts to AlxGa1−xN/GaN heterostructures has been investigated, focusing, in particular, on the impact of the AlGaN microstructure on the current transport at Gr/AlGaN interface. Two Al0.25Ga0.75N/GaN heterostructures with very different quality in terms of surface roughness and defectivity, as evaluated by atomic force microscopy (AFM) and transmission electron microscopy, were compared in this study, i.e., a uniform and defect-free sample and a sample with a high density of typical V-defects, which locally cause a reduction of the AlGaN thickness. Nanoscale resolution current voltage (I-V) measurements by an Au coated conductive AFM tip were carried out at several positions both on the bare and Gr-coated AlGaN surfaces. Rectifying contacts were found onto both bare AlGaN surfaces, but with a more inhomogeneous and lower Schottky barrier height (ΦB ≈ 0.6 …