Lithium and O in zircon have strong potential as diffusion chronometers for assessing thermal histories of magmatic and metamorphic systems, but their diffusion mechanisms remain controversial. Zircon populations erupted from El Chichón volcano, Chiapas, Mexico, often contain xenocrysts of detrital origin with juvenile overgrowth forming a natural diffusion boundary within individual crystals. High-spatial resolution O and Li isotope analyses, U–Pb and U–Th geochronology, and Li (along with Al and Y) scanning ion imaging were acquired to compare diffusion model timescales with those derived from radiometric dating. Oxygen isotopes in El Chichón zircon xenocrysts preserve source heterogeneities, with xenocrystic and juvenile domains of zircon being in O-isotopic disequilibrium with the melt at the time of eruption. Preservation of these heterogeneities is consistent with recently determined O-isotope diffusion parameters when crystal residence at magmatic temperatures is assumed over the 103–104 year timescales indicated by U–Th geochronology. Lithium concentration gradients across the same boundaries are sharp within the ~ 2–5 µm lateral resolution of the ion beam, whereas Li isotopic compositions for xenocrystic cores are homogeneous at δ7Li = + 7.8 ± 2.3‰ (1 standard error) and different from their putative source. Diffusive equilibration of Li isotopes in zircon is consistent with protracted magmatic crystal residence, but preservation of Li abundance heterogeneities is difficult to reconcile with evidence for recurrent high-temperature exposure of zircon in a highly active magmatic system. We speculate that Li partitioning in zircon is in part coupled to slow-diffusing trivalent cations, which can cause severe underestimation of diffusion timescales extracted from Li diffusion modeling.