The interaction of the northern Nazca and southwestern Caribbean oceanic plates with South America, and the collision of the Panama-Choco arc have significant implications on the evolution of the northern Andes. We integrate an alternative interpretation of the Nazca and Caribbean kinematics with the magmatic and deformation history in the region. The northeastward migration of the Caribbean plate caused a progressive change in the geometry of the subducting Farallon plate, causing flat-slab subduction throughout the late Eocene-late Oligocene, inhibition of magmatism and eastward migration of the Andean deformation. Meanwhile, the Paleocene-Eocene highly oblique convergence of the Caribbean plate against South America changed by the mid-Eocene, when the Caribbean plate began to migrate in an easterly direction. These events and the late Oligocene breakup of the Farallon plate, prompted a Miocene plate reorganization, with further plate fragmentation, changes in convergence obliquity, steepening of the subducting slabs and renewal of magmatism. This tectonics was complicated by the accretion of the Panama-Choco arc to South America, which was characterized by early Miocene subduction erosion of the forearc and trench advance, followed by breakoff of the subducting slab east of Panama and collisional tectonics from the middle Miocene. By 9 Ma the Coiba and Malpelo microplates were attached to the Nazca plate, resulting in an abrupt change in convergence directions, that correlates with the main pulse of Andean orogeny. During the late Pliocene, the Nazca slab broke, triggering the modern volcanism south of 5.5º N. Seismicity data and tomography support the proposed reconstruction.