Abstract A geological transect across the suture separating northwestern South America from the Panama Arc helps document the provenance and thermal history of both crustal domains and the suture zone. During middle Miocene, strata were being accumulated over the suture zone between the Panama Arc and the continental margin. Integrated provenance analyses of those middle Miocene strata show the presence of mixed sources that includes material derived from the two major crustal domains: the old northwestern South American orogens and the younger Panama Arc. Coeval moderately rapid exhumation of Upper Cretaceous to Paleogene sediments forming the reference continental margin is suggested from our inverse thermal modeling. Strata within the suture zone are intruded by ~12 Ma magmatic arc‐related plutons, marking the transition from a collisional orogen to a subduction‐related one. Renewed late Miocene to Pliocene acceleration of the exhumation rates is the consequence of a second tectonic pulse, which is likely to be triggered by the onset of a flat‐slab subduction of the Nazca plate underneath the northernmost Andes of Colombia, suggesting that late Miocene to Pliocene orogeny in the Northern Andes is controlled by at least two different tectonic mechanisms.