Multiphase nanomaterials are of increasing importance in material science. Providing reliable and statistically meaningful information on their average nanostructure is essential for synthesis control and applications. In this paper, we propose a novel procedure that simplifies and makes more effective the electron powder diffraction-based Rietveld analysis of nanomaterials. Our single step in-TEM method allows to obtain the instrumental broadening function of the TEM directly from a single measurement without the need for an additional X-ray diffraction measurement. Using a multilayer graphene calibration standard and applying properly controlled acquisition conditions on a spherical aberration-corrected microscope, we achieved the instrumental broadening of ±0.01 Å in terms of interplanar spacing. The shape of the diffraction peaks is modeled as a function of the scattering angle using the Caglioti relation, and the obtained parameters for instrumental broadening can be directly applied in the Rietveld analysis of electron diffraction data of the analyzed specimen. During peak shape analysis, the instrumental broadening parameters of the TEM are controlled separately from nanostructure-related peak broadening effects, which contribute to the higher reliability of nanostructure information extracted from electron diffraction patterns. The potential of the proposed procedure is demonstrated through the Rietveld analysis of hematite nanopowder and two-component Cu-Ni nanocrystalline thin film specimens.