Zircons from 14 compositionally variable granitic rocks were examined in detail using CL image-guided micro-analysis to unravel the complex magmatic history above the southward retreating Hellenic subduction zone system in the Aegean Sea. Previously published U-Pb ages document an episodic crystallisation history from 17 to 11 Ma, with peraluminous (S-type) granitic rocks systematically older than closely associated metaluminous (I-type) granitic rocks. Zircon O- and Hf isotopic data, combined with trace element compositions, are highly variable within and between individual samples, indicative of open-system behaviour involving mantle-derived melts and evolved supracrustal sources. Pronounced compositional and thermal fluctuations highlight the role of magma mixing and mingling, in accord with field observations, and incremental emplacement of distinct melt batches coupled with variable degrees of crustal assimilation. In the course of partial fusion, more fertile supracrustal sources dominated in the earlier stages of Aegean Miocene magmatism, consistent with systematically older crystallisation ages of peraluminous granitic rocks. Differences between zircon saturation and crystallisation temperatures (deduced from zircon Ti concentrations), along with multimodal crystallisation age spectra for individual plutons, highlight the complex and highly variable physico-compositional and thermal evolution of silicic magma systems. The transfer of heat and juvenile melts from the mantle varied probably in response to episodic rollback of the subducting lithospheric slab, as suggested by punctuated crystallisation age spectra within and among individual granitic plutons.