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ABSTRACT The topographic growth of the Eastern Cordillera in the northern Andes of Colombia is a critical event in the tectonic and paleogeographic evolution of the western Amazon Basin. Documentation of early orogenic growth is enabled through multi‐proxy provenance signatures recorded in the adjacent retro‐foreland basin. In broken foreland basins, basement highs interrupt the lateral continuity of facies belts and potentially mask provenance signals. The Putumayo Basin is a broken foreland basin in western Amazonia at ~1°–3° N, where the Florencia, Macarena, and El Melón‐Vaupes basement highs have compartmentalised discrete depocentres during basin development. This study presents new evidence from stratigraphic, conglomerate clast count, sandstone petrography, detrital zircon U–Pb geochronology and novel apatite detrital U–Pb age trace element geochemistry analyses. The results show that the southern Eastern Cordillera (i.e., Garzon Massif) and Putumayo Basin basement highs were initially uplifted during the Late Cretaceous coeval with the Central Cordillera, most likely associated with the collision of the Caribbean Large Igneous Province (CLIP). Distinctive facies distributions and provenance changes characterise the Putumayo Basin over a ~300 km distance from south to north, in the Rumiyaco Formation and Neme Sandstone. Detrital zircon U–Pb ages record a sharp reversal from easterly derived Proterozoic to westerly sourced late Mesozoic–Cenozoic Andean zircons derived principally from the Central Cordillera. Provenance signatures of the synorogenic Eocene Pepino Formation demonstrate the continued exhumation of the Eastern Cordillera as a second‐order source area. However, the emergence of the northern intraplate highs modulated the provenance signature due to the rapid unroofing of relatively thinner marine sedimentary cover strata that overlie the Putumayo basement, in comparison to the thicker sequences of the southern basin. The provenance data and facies distributions of the Oligocene–Miocene Orito Group were more heterogeneous due to strike‐slip deformation, associated with major plate tectonic reorganisation as the Nazca Plate subducted under the South American margin.