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.