Various crystallite size estimation methods were used to analyze X-ray diffractograms of spherical cerium dioxide and titanium dioxide anatase nanoparticles aiming to evaluate their reliability and limitations. The microstructural parameters were estimated from several integral breadth methods such as Scherrer, Monshi, Williamson–Hall, and their variants: (i) uniform deformation model, (ii) uniform strain deformation model, and (iii) uniform deformation energy density model. We also employed the size–strain plot and Halder–Wagner method. For this purpose, an instrumental resolution function of an Al2O3 standard was used to subtract the instrumental broadening to estimate the crystallite sizes and strain, and the linear regression analysis was used to compare all the models based on the coefficient of determination. The Rietveld whole powder pattern decomposition method was introduced for comparison purposes, being the best candidate to fit the X-ray diffraction data of metal-oxide nanoparticles. Refined microstructural parameters were obtained using the anisotropic spherical harmonic size approach and correlated with the above estimation methods and transmission electron microscopy images. In addition, µ-Raman spectra were recorded for each material, estimating the mean crystallite size for comparison by means of a phonon confinement model.