Chemical abrasion, a two-step process of annealing and partial dissolution, is routinely applied to zircon grains prior to U-Pb geochronology, to remove portions of the grains affected by Pb loss. The exact effect of this technique on the zircon structure and the distribution of radiogenic isotopes, however, remains elusive. Herein, grains of reference zircon OG1 were either fully or partially subjected to the chemical abrasion process and subsequently analysed by sensitive high mass resolution ion microprobe (SHRIMP) to determine the U-Pb systematics. Sputter craters from untreated, annealed, and fully chemically abraded aliquots were then mapped using Raman spectroscopy to determine the magnitude and distribution of radiation damage. For the untreated and annealed zircon, sputter craters from both concordant and discordant analyses were mapped. All chemically abraded zircon SHRIMP analyses were concordant. Raman mapping showed that the bottoms of discordant SHRIMP sputter craters generally had areas of higher and more heterogeneous Raman band width than concordant sputter pits for the same treatment. These results are consistent with previous scanning electron microscopy and micro computer tomography results. Based on the Raman maps, sputter craters with varying degrees of lattice damage and Pb loss were targeted for nanoscale analysis using atom probe tomography (APT) to assess the distribution of radiogenic isotopes at the lattice scale. APT reconstructions reveal a homogeneous distribution of all major components and radiogenic isotopes for all samples. These results indicate that APT is not able to detect elemental mobility or void formation arising from the lead loss, annealing or chemical abrasion in these samples. Thus the APT data do not provide additional constraints beyond the SHRIMP and Raman data on the mechanisms of Pb loss. Importantly, as the APT technique cannot distinguish between concordant and 5–10 % discordant zircon, it should not be used for this purpose.