Copper chalcogenides find applications in different domains including photonics, photothermal therapy and photovoltaics. CuTe nanocrystals have been proposed as an alternative to noble metal particles for plasmonics. Although it is known that deviations from stoichiometry are a prerequisite for plasmonic activity in the near-infrared, an accurate description of the material and its (optical) properties is hindered by an insufficient understanding of the atomic structure and the influence of defects, especially for materials in their nanocrystalline form. We demonstrate that the structure of Cu1.5±xTe nanocrystals can be determined using electron diffraction tomography. Real-space high-resolution electron tomography directly reveals the three-dimensional distribution of vacancies in the structure. Through first-principles density functional theory, we furthermore demonstrate that the influence of these vacancies on the optical properties of the nanocrystals is determined. Since our methodology is applicable to a variety of crystalline nanostructured materials, it is expected to provide unique insights concerning structure-property correlations.