Micrometeorites (MMs) retrieved from the Earth’s surface commonly undergo frictional heating as they enter the atmosphere. The compositional and textural effects of this heat-processing have been well documented and can be observed on the micrometre (μm)-scale, including the formation of iron-rich shells or the depletion of volatile elements, such as zinc. Atom probe tomography (APT) is a technique that has the capability to explore nanometre (nm)-scale features within such materials by producing three-dimensional (3D) compositional maps, displaying trends that may have been undetectable at lower resolutions. Here, we present the successful application of APT to an Antarctic MM, which we believe to be the first use of this technique on cosmic dust. From our MM sample, 11 tips were analysed from 2 sites, displaying nm-scale trends from the core to the rim. Many of the tips show interesting features, for example, one tip (A-M5) has a compositional boundary highlighted by clear elemental differences, consistent with core-rim partitioning, while a second tip (B-M1) shows evidence for a grain boundary adjacent to a carbon-rich region. We discuss our findings in the context of previously described processes, such as the presence of temperature gradients, which occur during atmospheric entry. We find evidence of thermal processing that we believe has caused nm-scale features along a textural boundary and heterogeneous elemental distributions, which may indicate unmelted material. These features may represent atmospheric entry indicators, which would suggest that entry processing affects MMs on the nm-scale. This could have implications for the delivery of sub-μm phases to planetary bodies via cosmic dust, and their survival during atmospheric entry.