The application of different methods for a microstructural analysis of functional catalysts is reported for the example of different Cu/ZnO-based methanol synthesis catalysts. Transmission electron microscopy and diffraction were used as complementary techniques to extract information on the size and the defect concentration of the Cu nano-crystallites. The results, strengths and limitations of the two techniques and of different evaluation methods for line profile analysis of diffraction data including Rietveld-refinement, Scherrer- and (modified) Williamson–Hall-analyses, single peak deconvolution and whole powder pattern modeling are compared and critically discussed. It was found that in comparison with a macrocrystalline pure Cu sample, the catalysts were not only characterized by a smaller crystallite size, but also by a high concentration of lattice defects, in particular stacking faults. Neutron diffraction was introduced as a valuable tool for such analysis, because of the larger number of higher-order diffraction peaks that can be detected with this method. An attempt is reported to quantify the different types of defects for a selected catalyst.