Description: Fluorine and chlorine X-ray count rates are known to vary significantly during electron probe microanalysis (EPMA) of apatite. Since the rate, timing, and magnitude of this variation are a function of apatite orientation and composition, as well as EPMA operating conditions, this represents a significant problem for volatile element analysis in apatite. Although the effect is thought to be an intrinsic crystallographic response to electron-beam exposure, the mechanisms and causes of the count rate variability remain unclear. We tackle this by examining directly the effects of electron-beam exposure on apatite, by performing secondary ion mass spectrometry (SIMS) depth profiles of points previously subject to electron-beam irradiation. During irradiation of fluorapatite, oriented with the c -axis parallel to the electron beam, halogens become progressively concentrated at the sample surface, even under a relatively low power (15 nA, 10–15 kV) beam. This surface enrichment corresponds to an observed increase in EPMA F K α X-ray count rates. After prolonged irradiation, the surface region starts to lose halogens and becomes progressively depleted, corresponding with a drop in EPMA count rates. Under normal EPMA operating conditions there is no halogen redistribution in fluorapatite oriented with the c -axis perpendicular to the electron beam, or in chlorapatite. We infer that anionic enrichment results from the migration of halogens away from a center of charge build-up caused by the implantation of electrons from the EPMA beam, assisted by the thermal gradient induced by electron-matter interactions. The process of surface enrichment is best explained by halogen migration through interstitial crystallographic sites in the c -axis channel. This suggests that once the thermal and electric fields are removed, halogens may relax back to their original positions on very long timescales or with sample heating.