Abstract The enhancement of the performance of advanced nitride-based optoelectronic devices requires the fine tuning of their composition, which has to be determined with a high accuracy and at the nanometer scale. For that purpose, we have evaluated and compared energy dispersive X-ray spectroscopy (EDX) in a scanning transmission electron microscope (STEM) and atom probe tomography (APT) in terms of composition analysis of AlGaN/GaN multilayers. Both techniques give comparable results with a composition accuracy better than 0.6 % even for layers as thin as 3 nm. In case of EDX, we show the relevance of correcting the X-ray absorption by simultaneous determination of the mass thickness and chemical composition at each point of the analysis. Limitations of both techniques are discussed when applied to specimens with different geometries or compositions.