Nanocrystals (NCs) present unique physicochemical properties arising from their size and the presence of ligands. Comprehending and controlling the ligand–crystal interactions as well as the ligand exchange process is one of the central themes in NC science nowadays. However, the relationship between NC structural disorder and the ligand exchange effect in the NC atomic structure is not yet sufficiently understood. Here we combine pair distribution function analysis from electron diffraction data, extended X-ray absorption fine structure, and high-resolution transmission electron microscopy as experimental techniques and first-principles density functional theory calculations to elucidate the ligand exchange effects in the ZrO2 NC structure. We report a substantial decrease in the structural disorder for ZrO2 NCs caused by strain rearrangements during the ligand exchange process. These results can have a direct impact on the development of functional nanomaterials, especially in properties controlled by s…