After more than a century of research, the chronology of the deformation of the external part of the western Alpine belt (France) is still controversial for the Miocene epoch. In particular, the poor dating of the foreland basin sedimentary succession hampers a comprehensive understanding of the deformation kinematics. Here we focus on the Miocene molasse deposits of the northern subalpine massifs, southern Jura, Royans, Bas-Dauphiné, Crest, and La Bresse sedimentary basins through a multidisciplinary approach to build a basin-wide tectono-stratigraphic framework. Based on sequence stratigraphy constrained by biostratigraphical, chemostratigraphical (Sr isotopes), and magnetostratigraphical data between the late Aquitanian (∼ 21 Ma) and the Tortonian (∼ 8.2 Ma), the Miocene molasse chronostratigraphy is revised with a precision of ∼ 0.5 Ma. The Miocene molasse sediments encompass four different paleogeographical domains: (i) the oriental domain outlined by depositional sequences S1a to S3 (∼ 21 to ∼ 15 Ma), (ii) the median domain characterized by sequences S2 to S5 (∼ 17.8 to ∼ 12 Ma), (iii) the occidental domain in which sequences S2a to S8 (∼ 17.8 to ∼ 8.2 Ma) were deposited, and (iv) the Bressan domain where sedimentation is restricted to sequences S6 to S8 (∼ 12 to ∼ 8.2 Ma). A structural and tectono-sedimentary study is conducted based on new field observations and the reappraisal of regional seismic profiles, thereby allowing the identification of five major faults zones (FZs). The oriental, median, and occidental paleogeographical domains are clearly separated by FZ1, FZ2, and FZ3, suggesting strong interactions between tectonics and sedimentation during the Miocene. The evolution in time and space of the paleogeographical domains within a well-constrained structural framework reveals syntectonic deposits and a westward migration of the depocenters, allowing for proposing the succession of three deformation phases at the western Alpine front. (i) The first is a compressive phase (P1) corresponding to thrusting above the Chartreuse oriental thrust (FZ1), which was likely initiated during the Oligocene and rooted east of Belledonne. This tectonic phase generated reliefs that limited the Miocene transgression to the east. (ii) The second is a ∼ WNW–ESE-directed compressive phase (P2) lasting between 18.05 ± 0.25 Ma and ∼ 12 Ma, with thrusts rooted in the Belledonne basal thrust. Thrusts were activated from east to west: the Salève (SAL) and Gros Foug (GF) thrusts and then successively FZ2, FZ3, FZ4, and FZ5. Along two WNW–ESE balanced cross sections the amount of horizontal shortening is of ∼ 6.3 to 6.7 km, corresponding to average shortening rates of ∼ 1.2 km Myr−1 and migration of the deformation toward the west at a rate of ∼ 2.9 km Myr−1. During ∼ 6 Myr, the Miocene Sea was forced to regress rapidly westwards in response to westward migration of the active thrusts and exhumation of piggyback basins atop the fault zones. Phase P2 thus deeply shaped the Miocene paleogeographical evolution of the area and appears as a prominent compressive phase at the scale of the western Alps from the Swiss molasse basin to the Rhodano–Provencal one. (iii) The third is a ∼ 300 m phase of uplift in the Bas-Dauphiné (P3) of probable Tortonian age (∼ 10 Ma), which would have induced southward sea retreat and been coeval with the folding of the Jura in the north and possibly with back-thrusting east of the Chartreuse massif.