The island of Naxos, Greece, has been previously considered to represent a Cordilleran-style metamorphic core complex that formed during Cenozoic extension of the Aegean Sea. Although lithospheric extension has undoubtedly occurred in the region since 10 Ma, the geodynamic history of older, regional-scale, kyanite- and sillimanite-grade metamorphic rocks exposed within the core of the Naxos dome is controversial. Specifically, little is known about the pre-extensional prograde evolution and the relative timing of peak metamorphism in relation to the onset of extension. In this work, new structural mapping is presented and integrated with petrographic analyses and phase equilibrium modeling of blueschists, kyanite gneisses, and anatectic sillimanite migmatites. The kyanite-sillimanite–grade rocks within the core complex record a complex history of burial and compression and did not form under crustal extension. Deformation and metamorphism were diachronous and advanced down the structural section, resulting in the juxtaposition of several distinct tectono-stratigraphic nappes that experienced contrasting metamorphic histories. The Cycladic Blueschists attained ∼14.5 kbar and 470 °C during attempted northeast-directed subduction of the continental margin. These were subsequently thrusted onto the more proximal continental margin, resulting in crustal thickening and regional metamorphism associated with kyanite-grade conditions of ∼10 kbar and 600–670 °C. With continued shortening, the deepest structural levels underwent kyanite-grade hydrous melting at ∼8–10 kbar and 680–750 °C, followed by isothermal decompression through the muscovite dehydration melting reaction to sillimanite-grade conditions of ∼5–6 kbar and 730 °C. This decompression process was associated with top-to-the-NNE shearing along passive-roof faults that formed because of SW-directed extrusion. These shear zones predated crustal extension, because they are folded around the migmatite dome and are crosscut by leucogranites and low-angle normal faults. The migmatite dome formed at lower-pressure conditions under horizontal constriction that caused vertical boudinage and upright isoclinal folds. The switch from compression to extension occurred immediately following doming and was associated with NNE-SSW horizontal boudinage and top-to-the-NNE brittle-ductile normal faults that truncate the internal shear zones and earlier collisional features. The Naxos metamorphic core complex is interpreted to have formed via crustal thickening, regional metamorphism, and partial melting in a compressional setting, here termed the Aegean orogeny, and it was exhumed from the midcrust due to the switch from compression to extension at ca. 15 Ma.