Determining the tectonic evolution and thermal structure of a tectonic unit that experiences a subduction-related pressure temperature (P-T) loop is challenging. Within a single unit, P-T conditions can vary from top to bottom which can only be revealed by detailed petrological work. We present micropetrological data from the middle section of the Cycladic Blueschist Unit (CBU) in Naxos, Greece, which indicates a different P-T loop than that for the top of the sequence. Using Zr-in-rutile and Ti-in-biotite thermometry coupled with quartz-in-garnet elastic barometry and phase equilibrium thermodynamic modeling, we identify a prograde path from 15.4 ± 0.8 kbar to 19.9 ± 0.6 kbar and from 496 ± 16 °C to 572 ± 7 °C (2σ uncertainty), equilibration during decompression at 8.3 ± 1.5 kbar and 519 ± 12 °C followed by near-isobaric heating to 9.2 ± 0.8 kbar and 550 ± 10 °C (or even 584 ± 19 °C), and a final greenschist-facies equilibration stage at 3.8 ± 0.3 kbar and 520 ± 4 °C. We compare these P-T estimates with published data from the top and also the bottom of the CBU section and find that the bottom half of the CBU on Naxos records higher peak high-pressure (HP) of about 4 kbar than the top of the unit, defining the thickness of the CBU section on Naxos to about 15 km in the Eocene. We determine that crustal thickening of up to ~15% occurs in the upper half of the CBU section during exhumation of the HP rocks in an extrusion wedge in a convergence setting. At about 30 Ma, the bottom half of the CBU was finally thrust onto the radiogenic Cycladic basement. Subsequently this bottom half of the CBU section underwent isobaric heating of 9–96 °C between c. 32–28 and 23–21 Ma. Isobaric heating occurred below the upper CBU section that thickened during decompression and commenced when HP metamorphism in the Cyclades ended. This suggests that thermal relaxation following tectonic accretion in the Cyclades controlled heating of the evolving Cycladic orogen during a tectonically quiescent period before lithospheric extension commenced by 23–20.5 Ma.