Allanite has the potential to be a useful chronometer of crustal evolution, forming in response to a wide spectrum of metamorphic and magmatic conditions and incorporating weight-percent concentrations of LREE, Th and U. Despite its growing use in in situ U–Th–Pb geochronology, allanite reference materials lack sufficient U–Th–Pb isotopic characterisation and little is known concerning the response of U–Th–Pb systematics of allanite to hydrothermal alteration and self-irradiation. This contribution presents the results of a combined ID-TIMS and LA-ICPMS U–Th–Pb study on a suite of five allanite crystals, spanning ∼2.6 Ga and including three commonly-used allanite reference materials: the Siss, Bona and Tara allanites. Siss and Bona allanites preserve an inherited ca. 1 Ga Pb component, consistent with the presence of xenocrystic allanite cores or the presence of zircon micro-inclusions. Tara allanite yields concordant U–Pb ages (407–430 Ma), but is affected by Th/U fractionation, likely caused by hydrothermal alteration. Additionally, the tendency for Th to become mobilised post-crystallisation is further evidenced by two Precambrian allanite megacrysts, LE40010 (ca. 2.8 Ga) and LE2808 (ca. 1.1 Ga), that both exhibit discordant Th/Pb analyses, linked to the formation of thorite micro-inclusions along hydration pathways. Self-irradiation dose versus discordance relationships show that a percolation threshold is present in allanite at cumulative dose values close to 3 × 1017 α-decay g−1, an order of magnitude smaller than zircon. Collectively, the presence of common-Pb and excess-206Pb, its susceptibility to incur Th/U fractionation and hydrothermal Pb-loss complicates the use of allanite as a geochronometer. These factors explain dispersion of ∼4% in the isotopic compositions of Siss and Tara allanites measured by LA-ICPMS, providing a fundamental limit on the accuracy of the allanite chronometer using these reference materials.