In Northwestern South America (NWSA) the geodetic data show a consistent northeastward displacement of blocks, while the geological record shows a predominant shortening in NW-SE direction suggesting a clear pattern of strain partitioning. This type of deformation has been extensively studied in the context of two convergent plates. However, in NWSA this is complicated by the interaction of multiple tectonic elements, including the Caribbean and Farallon/Nazca plates and the accretion of the Panama-Choco Arc. In this study we integrate the plate convergence evolution with multiple lines of evidence in the geological record, to propose a tectonic reconstruction that accounts for the deformation distribution during the Cenozoic. Our results indicate that deformation was not spatially homogeneous nor did it occur continuously during the Cenozoic. The main drivers of these variations were variations of convergence obliquity of the involved plates, the presence of heterogeneous lithospheric strength zones, changes in the geometry of the subducting slabs and the transition from subduction to collisional tectonics of the Panama-Choco Arc against NWSA. The obtained relative motion of blocks reproduces a strain evolution that is consistent with the different episodes of deformation reported in the literature. The model is additionally supported by the reconstructed velocity and strain vectors, which have a good match with equivalent indicators of the recent deformation in NWSA. Furthermore, the integration of the proposed palinspastic model with existing paleoenvironmental models, allowed us to construct restored paleogeographic maps that agree well with the deformation and exhumation history of the Northern Andes.