The goal of this paper is to use the structural, metamorphic and geochronological record from the migmatitic core of the Naxos dome (Greece) and its associated subdomes to address the internal dynamics of a partially molten orogenic root. U-Pb ages from ca. 24 to 16 Ma and textures of zircon in the migmatites suggest successive dissolution and precipitation cycles with a period of 1 to 2 Ma, interpreted as the timescale of convective instabilities in a ca. 20 km thick partially molten layer. Dimensional analysis indicates that convection of this root requires a viscosity lower than 1018 Pa·s, consistent with viscosity values expected for partially molten felsic rocks. Structural analysis and U-Pb geochronology of deformed granitic dikes rooting in the migmatites record the subsequent development of the Naxos dome by diapirism from ca. 16 to 13 Ma. The size of the first order migmatite dome on Naxos (5 × 12 km) requires that the unstable layer at the onset of diapirism was 5 to 10 km thick and presented a moderate viscosity contrast with its envelope. From this analysis we propose that the Naxos migmatite dome documents a two stage dynamic evolution for the partially molten root of the Aegean belt characterized by (1) crustal scale convection for at least 8 Ma and (2) diapirism for about 3 Ma during progressive thinning of the collapsing orogenic crust.