Doping graphene by heteroatoms such as nitrogen presents an attractive route to control the position of the Fermi level in the material. We prepared N-doped graphene on Cu (111) and Ir (111) surfaces via chemical vapor deposition of two different molecules. Using scanning tunneling microscopy images as a benchmark, we show that the position of the dopant atoms can be determined using atomic force microscopy. Specifically, the frequency shift–distance curves Δ f (z) acquired above a N atom are significantly different from the curves measured over a C atom. Similar behavior was found for N-doped graphene on Cu (111) and Ir (111). The results are corroborated by density functional theory calculations employing a van der Waals functional.