The relationship between subduction dynamics and crustal deformation in the Mediterranean region has been recently studied using three-dimensional (3D) numerical models. Such models require, however, a detailed information concerning the past geological evolution. We use stratigraphic, petrologic, metamorphic, structural, paleomagnetic and magmatic data to build new kinematic reconstructions of the eastern Mediterranean region since the late Cretaceous using the principle of non-rigid domains. The motions of the 56 deforming domains defined in this work are calculated based on published paleomagnetic rotations, the directions and amounts of displacement on crustal-scale shear zones and the burial and exhumation histories of the main metamorphic units. Extracted from these reconstructions, paleotectonic maps and lithospheric-scale cross-sections illustrate that the present-day subduction zone has been continuously retreating southward since the late Cretaceous and has accreted several small continental domains in the process. We find evidence for two back-arc-related extensional events: (1) slow extension along the Balkans and the Pontides in the late Cretaceous while the trench was long and linear and (2) faster extension in the Rhodope-Aegean-west Anatolian region since the Eocene-Oligocene. Rapid rotation of the Hellenides between 15 and 8 Ma probably indicates a slab tearing event below western Anatolia that could have further accelerated this extensional kinematics. Spatial distribution and the geochemical signature of magmatic centers integrated in these reconstructions allow us to trace mantle-related processes revealing the deep dynamics that controls both the magma genesis and the crustal deformation.