Investigating how grain structure affects the functional properties of nanoparticles requires a robust method for nanoscale grain mapping. In this study, we directly compare the grain mapping ability of transmission Kikuchi diffraction (TKD) in a scanning electron microscope to automated crystal orientation mapping (ACOM) in a transmission electron microscope across multiple nanoparticle materials. Analysis of well-defined Au, ZnO, and ZnSe nanoparticles showed that the grain orientations and GB geometries obtained by TKD are accurate and match those obtained by ACOM. For more complex polycrystalline Cu nanostructures, TKD provided an interpretable grain map whereas ACOM, with or without precession electron diffraction, yielded speckled, uninterpretable maps with orientation errors. Acquisition times for TKD were generally shorter than those for ACOM. Our results validate the use of TKD for characterizing grain orientation and grain boundary distributions in nanoparticles, providing a framework for the broader exploration of how microstructure influences nanoparticle properties.