Reconstructing the original geometry of a high-pressure tectonic unit is challenging but important to understand the mechanisms of mountain building. While a single nappe is subducted and exhumed, nappe-internal thrusts may disrupt it into several subunits. The Middle-CBU nappe of the Cycladic Blueschist Unit (Hellenide subduction orogen, Greece) shows evidence of such disruption along a Trans-Cycladic-Thrust (TCT), however, the timing of this thrusting is unknown. Here, we report multi-petrological and geochronological data from the Middle-CBU nappe from the Thera and Ios islands (Greece). Using Zr-in-rutile thermometry coupled with quartz-in-garnet elastic barometry, average P–T and phase equilibrium thermodynamic modelling, we show that garnet growth in Ios occurred during prograde metamorphism at 6.7 ± 1.4 kbar to 13.0 ± 1.6 kbar and 326 ± 20°C to 506 ± 13°C (2σ uncertainty) followed by early exhumation to 10.1 ± 0.6 kbar and 484 ± 14°C and a greenschist facies overprint at 5.7 ± 1.2 kbar and 416 ± 14°C. For Thera, we constrain peak HP conditions of 7.6 ± 1.8 kbar and 331 ± 18°C, followed by exhumation and equilibration at ~2 kbar and ~275°C using average P–T and phase equilibrium thermodynamic modelling. For Ios, Uranium-Pb garnet geochronology provides ages of 55.7 ± 5.0 Ma (2σ uncertainties) for prograde and 40.1 ± 1.4 Ma for peak HP metamorphism. Combining our new P–T–t data from Thera and Ios islands with existing data from Naxos island, we conclude that the studied nappe segments represent remnants of a former coherent nappe. The P–T–t data define an Eocene subduction rate of 2.1 ± 1.0 km/Ma, which is distinctly slower than the current subduction rate of 40–45 km/Ma. After subduction, the exhumation of the Middle-CBU nappe occurred during the Oligocene at different rates for different localities. The Middle-CBU nappe of Naxos was exhumed at a rate of ~6 km/Ma, contrasting with the exhumation rate of ~3 km/Ma calculated for Ios. This result suggests that the Middle-CBU nappe of Naxos rocks was thrust on the Ios one during the Oligocene. Using P–T–t data and assuming realistic subduction angles during the Eocene and the Oligocene, we present a 2D structural reconstruction of the Middle-CBU nappe of these islands. This reconstruction helps to understand the mechanisms of subduction of a continental margin and its disruption during exhumation.