The Miocene of the Western Alpine foreland basin were deposited in a north–south seaway along the active alpine orogenic front. In the subalpine massifs and the southern Jura mountains, the revised Miocene stratigraphy documents a detailed chronology of thrust propagation at the western alpine front, where tectonic activity had a primary influence on seaway palaeogeographical evolution. Here we propose nine palaeogeographical maps during the Miocene, the first of which depicts the initial Miocene transgression at c. 21.0 Ma. Between c. 18.05 and c. 12.0 Ma, a westward retreat of the Miocene Sea occurred in response to activation of the basal thrust of the Belledonne massif, which in turn triggered successive fault zones from east to west. At c. 10.0 Ma, a major uplift phase intervened and induced a rapid southward retreat of the Miocene Sea. The reconstructed palaeogeographical maps outline the main controls on the foreland basin seaway evolution: (1) the timing of the main thrusts; (2) the inherited palaeotopography; and (3) eustatic sea-level changes during the Miocene. These reconstructions are integrated at the basin scale, highlighting the southward- to westward-directed seaway migration in response to the Belledonne thrust activity that deeply shaped the palaeogeographical evolution during the early to middle Miocene.