Deformation of the Eastern Cordillera, as a double-verging thrust belt that separates the Magdalena Valley from the Llanos Basin, is a defining moment in the history of the northern Andes in South America. Here we examine the age and depositional setting of the youngest stratigraphic unit in three sectors of the Eastern Cordillera: (i) the Santa Teresa Formation (western flank), (ii) the Usme Formation (southern central axis), and (iii) the Concentración Formation (northeastern central axis). These units were deposited prior to the main Neogene deformation events. They represent the last preserved record of lowland conditions in the Eastern Cordillera, and they are coeval with a thick syn-orogenic deposition reported in the Llanos Basin and Magdalena Valley. Based on palynological data, we conclude that the upper Usme Formation was deposited during the Bartonian-earliest Rupelian? (Late Eocene-earliest Oligocene?); the Concentración Formation was deposited during the Late Lutetian-Early Rupelian (Middle Eocene to Early Oligocene), and the upper Santa Teresa Formation was accumulated during the Burdigalian (Early Miocene). These ages, together with considerations on maximum post-depositional burial, provide important time differences for the age of initial uplift and exhumation along the axial zone and western foothills of the Eastern Cordillera. The switch from sediment accumulation to erosion in the southern axial zone of the Eastern Cordillera occurred during the Rupelian-Early Chattian (Oligocene, ca 30 to ca 26 Ma), and in the northeastern axial zone occurred prior to the latest Chattian-Aquitanian (latest Oligocene-Early Miocene ca 23 Ma). In contrast, in the western flank, the switch occurred during the Tortonian (Late Miocene, ca 10 Ma). In addition, we detected a marine transgression affecting the Usme and Concentración formations during the Late Eocene; coeval marine transgression has been also documented in the Central Llanos Foothills and Llanos Basin, as evidenced by the similarity in floras, but not in the western foothills. Our dataset supports previous sedimentological, geochemical and thermochronological works, which indicated that (i) deformation in the Eastern Cordillera was a diachronous process, (ii) the sedimentation along the axial zone stopped first in the south and then in the north during the Oligocene, (iii) depositional systems of the axial zone and central Llanos Foothills kept partly connected at least until the Late Eocene, and (iv) Miocene strata were only recorded in adjacent foothills as well as the Magdalena and Llanos basins.