Accessory mineral U-Pb geochronometers are crucial tools for constraining the timing of deformation in a wide range of geological settings. Despite the growing recognition that intragrain age variations within deformed minerals can spatially correlate to zones of microstructural damage, the causal mechanisms of Pb loss are not always evident. Here, we report the first U-Pb data for shock-deformed xenotime, from a detrital grain collected at the Vredefort impact structure in South Africa. Orientation mapping revealed multiple shock features, including pervasive planar deformation bands (PDBs) that accommodate up to 40° of lattice misorientation by <100>{010} slip, and also an ~50-µm-wide intragrain shear zone that contains {112} deformation twin lamellae in two orientations. Twenty-nine in situ secondary ion mass spectrometry (SIMS) U-Pb analyses from all microstructural domains yielded a well-defined discordia with upper-intercept age of 2953 ± 15 Ma (mean square of weighted deviates [MSWD] = 0.57, n = 29, 2σ), consistent with derivation from Kaapvaal craton bedrock. However, the 1754 ± 150 Ma lower concordia intercept age falls between the 2020 Ma Vredefort impact and ca. 1100 Ma Kibaran orogenesis and is not well explained by multiple Pb-loss episodes. The pattern and degree of Pb loss (discordance) correlate with increased [U] but do not correlate to microstructure (twin, PDB) or to crystallinity (band contrast) at the scale of SIMS analysis. Numerical modeling of the Pb-loss history using a concordia-discordia-comparison (CDC) test indicated that the lower concordia age is instead best explained by an alteration episode at ca. 1750 Ma, rather than a multiple Pb-loss history. In this example, the U-Pb system in deformed xenotime does not record a clear signature of impact age resetting; rather, the implied high dislocation density recorded by planar deformation bands and the presence of deformation twins facilitated subsequent Pb loss during a younger event that affected the Witwatersrand basin. Microstructural characterization of xenotime targeted for geochronology provides a new tool for recognizing evidence of deformation and can provide insight into complex age data from highly strained grains, and, as is the case in this study, elucidate previously unrecognized alteration events.