Subduction orogens grow by accretion of slices of continental lithosphere scraped off the downgoing slab. Although seismological and geophysical data now illuminate the deep structure of these orogens, understanding deep crustal underplating dynamics remains challenging. This study focuses on the Albanides, a subduction orogen in the central‐eastern Mediterranean, formed by the accretion of continental material during the eastward subduction of Adria beneath Eurasia. The thickening at depth of the crustal edifice occurred along with the development of a shallow fold‐and‐thrust belt. This process involved the deposition of progressively younger syn‐orogenic deposits as deformation migrated SW‐ward from the Cretaceous to the Miocene. To explore the relationship between deep‐seated structures and surface deformation, we investigate the recent crustal thickening of the Albanides using low‐temperature thermochronology and 3D thermokinematic modeling of a seismically constrained crustal section. Our data reveal a pulse of exhumation during the latest Miocene‐Pliocene, amounting to approximately 3–4 km, which we propose has been driven by a deep‐seated thrust system imaged by receiver function images. These inferences have significant implications for understanding the interactions between deep and shallow crustal processes and their role in shaping the Albanides. Furthermore, they provide insights into the timing and kinematics of subduction‐related orogenic processes and, potentially, on the separation of the Adria plate from Africa.