Abstract: The trace-element composition of zircon can be used to constrain magma-source characteristics, crystallization environments, and subsequent geological processes. In practice, however, conventional in situ analytical techniques are limited to spot sizes at the submicrometer scale or larger. Consequently, individual measurements may integrate signals from complex internal features, including oscillatory zoning, sector zoning, inclusions, and fine precipitates, making it difficult to resolve elemental distributions at smaller spatial scales. To investigate the nanoscale distribution and zoning-related variations of trace elements in zircon, a single Plešovice zircon grain was examined using cathodoluminescence (CL) imaging, backscattered-electron (BSE) imaging, and atom probe tomography (APT). These techniques were combined to characterize the trace-element compositions and three-dimensional spatial distributions of distinct structural domains within the grain. Trace elements in needle specimens prepared from the CL-dark and CL-bright domains were generally homogeneously distributed at the nanoscale. However, the two domains differed in their concentrations of U, Th, Y, P, Dy, Al, and Hf, with relative concentration trends consistent with those previously observed at the micrometer scale. BSE imaging revealed an approximately 2 μm monazite inclusion and two regions with heterogeneous BSE contrast, each approximately 30–50 μm across. The latter contained micrometer-scale, BSE-bright precipitates enriched in Ca and P within a dark matrix. APT analysis of a needle specimen prepared from the dark matrix revealed that trace elements were present at generally elevated concentrations and exhibited layered distributions at the nanoscale, indicating that this domain records non-equilibrium crystallization associated with phosphate-phase precipitation. These results demonstrate that APT enables direct characterization of nanoscale trace-element distributions in zircon, thereby linking micrometer-scale structural observations to atomic-scale elemental distributions. Nevertheless, oxygen loss and mass-spectral peak overlaps can compromise the accuracy of absolute trace-element concentration measurements. Further optimization of experimental parameters, more precise mass-spectrum calibration, and improved peak-deconvolution workflows are therefore required to enhance the reliability of quantitative APT analyses.