Basins around the margin of the Puna Plateau in NW Argentina each record the onset over a few hundred thousand years of alluvial-fan facies sedimentation with the deposition of the Punaschotter conglomerates in the late Cenozoic, despite differing tectonic histories. Their striking similarity suggests that these conglomerates might have a common origin, such as the climatically driven coarsening and increase in sedimentation rate proposed to have occurred worldwide at 4–2 Ma. With this contribution, we present new U-Pb geochronology of intercalated ashes that bracket the onset of Punaschotter deposition along the margin of the Puna Plateau in the Fiambalá and El Cajon Basins. Combining this with existing data, we explore the relative roles of climate and tectonics in shaping sedimentation in this region. Our analysis reveals that Punaschotter deposition was diachronous and only occurred if both aridity and structural deformation were present. Development of orographic barriers and global climate change may have contributed to establishing regional aridity. In the eastern part of the study region (Santa Maria and Angastaco), onset of Punaschotter deposition tracks the establishment of aridity. In the already arid western basins (Fiambalá, Corral Quemado), a reactivation of structural deformation may have triggered the onset of Punaschotter deposition. Our study shows that initiation of coarse alluvial facies in this part of the Andes largely preceded the 4–2 Ma global climate change and emphasizes the coupled nature of local climate and tectonics in controlling sedimentation.