The Takidani Pluton in Central Japan is one of the youngest exposed plutons in the world. It presents a sub-volcanic magmatic reservoir that is associated with voluminous caldera-forming eruptions including the Nyukawa PFD and Chayano–Ebisutoge PD. The pluton is vertically zoned comprising at least six distinct lithological units of granodiorites and granites. Textural and geochemical evidence for melt extraction from a crystal-rich magma is preserved in the upper section of the pluton. Thermodynamic simulations and thermal modelling suggest that rhyolitic magma had sufficient time to segregate before solidification supporting an origin by fractional crystallisation. Geochemical analyses, however, indicate that the generation of the rhyolites of the Chayano–Ebisutoge PD was dominated by crustal melting processes. The Takidani Pluton and the dacitic Nyukawa PFD are petrogenetically linked supporting conceptual models of crystal mush remobilisation. This study provides new insights into the magmatic plumbing systems of large caldera-forming eruptions.