Energy dispersive X-ray spectroscopy (EDX) in scanning transmission electron microscopy and atom probe tomography are used to characterize N-polar InGaN/GaN quantum wells at the nanometer scale. Both techniques first evidence the incorporation of indium in the initial stage of the barrier layer growth and its suppression by the introduction of H2 during the growth of the barrier layer. Accumulation of indium at step edges on the vicinal N-polar surface is also observed by both techniques with an accurate quantification obtained by atom probe tomography (APT) and its 3D reconstruction ability. The use of EDX allows for a very accurate interpretation of the APT results complementing the limitations of both techniques.