The rhyodacitic magma discharged during the 30–80 km3 DRE (dense rock equivalent) Late Bronze Age (LBA; also called ‘Minoan’) eruption of Santorini caldera is known from previous studies to have had a complex history of polybaric ascent and storage prior to eruption. We refine the timescales of these processes by modelling Mg–Fe diffusion profiles in orthopyroxene and clinopyroxene crystals. The data are integrated with previously published information on the LBA eruption (phase equilibria studies, melt inclusion volatile barometry, Mg-in-plagioclase diffusion chronometry), as well as new plagioclase crystal size distributions and the established pre-LBA history of the volcano, to reconstruct the events that led up to the assembly and discharge of the LBA magma chamber. Orthopyroxene, clinopyroxene and plagioclase crystals in the rhyodacite have compositionally distinct rims, overgrowing relict, probably source-derived, more magnesian (or calcic) cores, and record one or more crystallization (plag ≫ opx > cpx) events during the few centuries to years prior to eruption. The crystallization event(s) can be explained by the rapid transfer of rhyodacitic melt from a dioritic/gabbroic region of the subcaldera pluton (mostly in the 8–12 km depth range), followed by injection, cooling and mixing in a large melt lens at 4–6 km depth (the pre-eruptive magma chamber). Since crystals from all eruptive phases yield similar timescales, the melt transfer event(s), the last of which took place less than 2 years before the eruption, must have involved most of the magma that subsequently erupted. The data are consistent with a model in which prolonged generation, storage and segregation of silicic melts were followed by gravitational instability in the subcaldera pluton, causing the rapid interconnection and amalgamation of melt-rich domains. The melts then drained to the top of the pluton, at fluxes of up to 0.1–1 km3 year− 1, where steep vertical gradients of density and rheology probably caused them to inject laterally, forming a short-lived holding chamber prior to eruption. This interpretation is consistent with growing evidence that some large silicic magma chambers are transient features on geological timescales. A similar process preceded at least one earlier caldera-forming eruption on Santorini, suggesting that it may be a general feature of this rift-hosted magmatic system.