Meta‐peridotites outcropping at different structural levels within the Alpine metamorphic complex of the Cycladic island of Naxos were studied to re‐examine their metamorphic evolution and possible tectonic mechanisms for emplacement of mantle material into the continental crust. The continental margin section exposed on Naxos, consisting of pre‐Alpine basement and c. 7 km thick Mesozoic platform cover, has undergone intense metamorphism of Alpine age, comprising an Eocene (M1) blueschist event strongly overprinted by a Miocene Barrovian‐type event (M2). Structural concordance with the country rocks and metasomatic zonation at the contact with the felsic host rocks indicate that the meta‐peridotites have experienced the M2 metamorphism. This conclusion is supported by the similarity between metamorphic temperatures of the ultrabasic rocks and those of the host rocks. Maximum temperatures of 730–760 °C were calculated for the upper‐amphibolite facies meta‐peridotites (Fo–En–Hbl–Chl–Spl), associated with sillimanite gneisses and migmatites. Relict phases in ultrabasics of different structural levels indicate two distinct pre‐M2 histories: whereas the cover‐associated horizons have been affected by low‐grade serpentinization prior to metamorphism, the basement‐ associated meta‐peridotites show no signs of serpentinization and instead preserve some of their original mantle assemblage. The geochemical affinities of the two groups are also different. The basement‐associated meta‐peridotites retain their original composition indicating derivation by fractional partial melting of primitive lherzolite, whereas serpentinization has led to almost complete Ca‐loss in the second group. The cover‐associated ultrabasics are interpreted as remnants of an ophiolite sequence obducted on the adjacent continental shelf early in the Alpine orogenesis. In contrast, the basement‐associated meta‐peridotites were tectonically interleaved with the Naxos section at great depth during the Alpine collision and high P/T metamorphism. Their emplacement at the base of the orogenic wedge is inferred to have involved isobaric cooling from temperatures of c. 1050 °C within the spinel lherzolite field to eclogite facies temperatures of c. 600 °C.