Zircon petrochronology is widely used to quantify the age and duration of magma emplacement and differentiation. However, in highly differentiated magmas, such as those forming rare-metal granites, zircon may form at the magmatic–hydrothermal transition, and its primary crystallisation history, together with its secondary hydrothermal overprint, needs to be resolved and clarified. To resolve zircon formation in such evolved and mineralised granitic systems, we investigated heterogeneous zircons from the Beauvoir rare-metal granite (Massif Central, France). Most of the Beauvoir zircons are characterised by the presence of two distinct domains, designated as Zone 1 and Zone 2. Zone 1 occurs as rounded, Si- and Zr-rich domains, which are embedded in the interconnected Si- and Zr-poor Zone 2 domains that are also extremely P-, U-, F-, Ca-, Fe- and Mn-rich. Both of these zones are strongly damaged (metamict) by radioactive decay, mainly from their high U concentrations. Textures and chemical composition strongly suggest that Zone 1 corresponds to magmatic zircon that has been partly replaced by the Zone 2 material during the magmatic–hydrothermal transition. The crystallisation of Zone 1 zircon is preceded by the crystallisation of U-rich cores (∼6 wt % UO2) containing UO2 (uraninite) micro-inclusions, which are then surrounded by a Zone 1 homogeneous rim. These uraninite micro-inclusions resulted from the uranium migration in the metamict and amorphous precursor zircon. U-Pb dating of single zircon grains using chemical abrasion, isotope dilution thermal ionisation mass spectrometry (CA-ID-TIMS) techniques yielded a well-defined discordia line with an upper intercept at 312±2.9 (7.2) Ma (2σ) and a near-zero-age lower intercept. The discordancy reflects the continuous loss of radiogenic lead from a heavily damaged and aperiodic zircon lattice. On the other hand, ID-TIMS data from magmatic apatite of the Beauvoir granite yielded an age of 313.4±0.2 (1.3) Ma (2σ), so far, the most accurate and precise crystallisation age of the Beauvoir granite. Thus, we emphasise that although the study of zircon from highly differentiated systems provides strong insights into the magmatic–hydrothermal transition of these objects, their metamict nature prevents their use to precisely and accurately date the emplacement of rare-metal granite.