Within deforming continental regions where metamorphic core complexes (MCCs) and synextensional granitoids are closely associated, deciphering the link between detachment faulting and magmatism often remains complex as (1) the rheological weakness of magma may stimulate mechanisms of strain localization, and conversely, (2) tectonic processes may open/close drains where magmas can intrude. Here we tackle this issue by focusing on the Cyclades with the comparison of five granitoid-cored MCCs (Tinos, Mykonos, Ikaria, Naxos, and Serifos) and their flanking detachment systems. In this region, granitoids were emplaced into the middle/upper crust over a relatively short time period (15–9 Ma), while metamorphic domes were largely exhumed after more than 10 Myr of extension. None of those intrusions thereby proves to be a real candidate for the genesis of MCCs but would rather be a consequence of a warmer regime during lithospheric thinning. However, all collected structural and kinematic data converge toward a regional scheme in which magmatic activity played a more pivotal role than previously postulated. Indeed, late evolution stages of MCCs were dynamically impacted by intrusions along which local and transient heterogeneities of the mechanical strength occurred, interfering with the sequential development of detachments. During their tectonically controlled emplacement, magmatic products intruded already formed detachments at depth, locally inhibiting their activity, associated with a contemporaneous upward migration of extensional deformation that tended to localize through time within intrusion roofs along rheological discontinuities. The newly formed detachments are expressed within granitoids through a continuum of deformation from comagmatic to ductile conditions, followed by cataclasis along detachments.