Abstract Based on geological and tectonic investigations carried out along an N–S coast-to-coast transect across central Crete, southern Aegean (Greece), new meso- and macro-structural data mainly collected from Neogene–Quaternary deposits are presented and discussed. The occurrence of large-scale folds and thrusts together with diffuse minor contractional structures, as well as the overall geometry of the fault-bounded sedimentary basins document the persistence of a Tortonian–Early Pleistocene contractional regime, characterized by an NNW–SSE to NNE–SSW shortening direction and affecting the upper crust. This contractional event(s) was associated with the ongoing Hellenic subduction and caused the development of a southwards migrating out-of-sequence thrust system consisting of both reactivated inherited structures and new ones. The new data emphasize the importance and the extent of this contractional event intervening between the Early–Middle Miocene exhumation phase and the still active upper crustal extensional regime that was resumed in the island only during Pleistocene when the region was affected by diffuse normal faulting. While the contractional event was likely due to a stronger coupling along the overall subduction system, the onset of the new extensional stress conditions was probably related to a sudden southwards jump of the basal detachment along the lithospheric African subduction that caused a general stress release in the uppermost crust.