Ceria (CeO2) nanocrystals have unique and highly attractive properties that depend on the morphology and structure. In this paper, we demonstrate that by controlling the addition of copper to growing ceria nanocrystals it is possible to modulate the resulting structure properties. We show also by means of X-ray diffraction, high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray fluorescence spectrometry, and X-ray absorption spectroscopy that copper configuration affects both the morphology and the electronic structure of cerium oxide nanocrystals. Indeed, external and internal copper doping on ceria nanocrystals leads to structural transitions, including a morphological transition from cubic to truncated octahedron, along with cerium valence changes. The results of this study, optimizing the structural properties of such nanocrystals, may certainly trigger new opportunities and, ultimately, new applications.