New biostratigraphic zonations, core descriptions, sandstone petrography, fades analysis, and seismic information are compared with published detrital and bedrock geo- and thermochronology to build a Cenozoic paleogeographic reconstruction of the Andean retroarc region of Colombia, encompassing the ancestral Central Cordillera, Middle Magdalena Valley, Eastern Cordillera, and Llanos basin. We identify uplifted sediment source areas, provenance domains, depositional environments, and thickness changes to propose a refined paleogeographic evolution of eastern Colombia. We conclude that Cenozoic evolution of the northernmost Andes includes (1) a period of contractional deformation focused in the Central Cordillera and Middle Magdalena Valley that may have started by the Late Cretaceous, although thermochronological data points to maximum shortening and exhumation during the late Paleocene; (2) a period of slower deformation rates or even tectonic quiescence during the middle Eocene; and (3) a renewed phase of contractional deformation from the late Eocene to the Pleistocene/Holocene expressed in provenance, bedrock thermochronology, and increased subsidence rates in the Llanos foreland. The sedimentary response in the Llanos foreland basin is controlled by source area proximity, exhumation and shortening rates, relationships between accommodation and sediment supply, as well as potential paleoclimate forcing. This new reconstruction changes the picture of Cenozoic basin evolution offered by previous reconstructions, providing an updated chronology of deformation, which is tied to a more precise understanding of basin evolution.