Subduction margins are the loci of a wide range of deformation processes occurring at different timescales along the plate interface and in the overriding forearc crust. Whereas long-term deformation is usually considered as stable over Myr-long periods, this vision is challenged by an increasing number of observations suggesting a long-term pulsing evolution of active margins. To appraise this emerging view of a highly dynamic subduction system and identify the driving mechanisms, detailed studies on now-exhumed, high pressure-low temperature (HP-LT) accretionary complexes are crucial as they open a window on the deformation history from the plate interface to the surface. In this study, we combine structural and petrological observations, Raman spectroscopy on carbonaceous material, Rb/Sr multi-mineral geochronology and thermo-mechanical numerical models to unravel with an unprecedented resolution the tectono-metamorphic evolution of the Late-Cenozoic HP-LT nappe stack cropping out in western Crete (Hellenic subduction zone). A consistent decrease of peak temperatures and deformation ages toward the base of the nappe pile allows us to identify a minimum of three basal accretion episodes between ca. 28 Ma and ca. 15 Ma. On the basis of structural evidences combined with numerical modeling results, we argue that this succession of mass-flux events triggered (i) pulses in the strain rate, sometimes associated with a switch of the stress regime (i.e., compressional/extensional) and (ii) vertical surface oscillations eventually resulting in the growth of a high forearc topography. This accretion-controlled, Myr-scale tectonic and topographic signal plays a part in active deformations monitored at subduction margins, though it may remain invisible to most of geodetic methods because of superimposed shorter- timescale transients, such as seismic-cycle-related events.