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The Southern Patagonian Andes at the latitude of the Chile Triple junction in Argentina and Chile (46°–47.5°S) are the object of an ongoing discussion regarding their orogenic evolution in terms of tectonic crustal thickening and exhumation. Recent works point to an Early Cretaceous onset of shortening according to observations in foreland sequences. The ensuing Cenozoic thermal history of the region was influenced by increased shortening, oceanic‐ridge collision and formation of asthenospheric windows in a dynamic subduction setting. Furthermore, the onset of Patagonian glaciations after 7 Ma added increased complexities to the analysis of the main drivers of crustal cooling in this region. We applied zircon (U‐Th)/He and apatite fission track thermochronometry, and inverse thermal modeling to unravel the thermal history throughout different structural domains of the Patagonian Andes. New thermochronological data and thermal models showed a previously unrecognized set of Cretaceous cooling ages (120‐80 Ma) toward the foreland, that we relate to the onset of contraction during initial tectonic inversion. Toward the hinterland, Cenozoic cooling ages predominate, and are related to Oligocene‐Miocene contraction in response to increased subduction velocities. Based on the regional distribution of thermochronological ages and on results from thermal modeling, a resetting of the zircon (U‐Th)/He and apatite fission track systems in response to crustal heating related to the formation of an asthenospheric window after 16 Ma appears unlikely. After 7 Ma cooling rates increased in response to enhanced glacial erosion. In this work, we have used thermochronometers, basically clocks that start recording time once a rock‐sample has crossed a given temperature in the crust, to track the cooling of rock‐samples from the Patagonian Andes between 46.5°S and 48°S. In this area, several processes influenced the evolution of the landscape such as mountain building, glaciers erosion, and deep‐seated processes within the mantle. All of them may have left a trace in thermochronometers. Our goal is to determine the role of mountain building processes in rock cooling in this area. Our results suggest that rocks cooled in response to mountain building during the Cretaceous in what could be considered the first phase of construction of the Andes in the area. Mountain building processes continued influencing rock cooling during the Miocene, nearly 100 million‐years after the first phase. During the last 7 million‐years before the present, the onset of glacial erosion enhanced rock cooling. Finally, we found no records that the rocks heated in response to deep‐seated mantle processes. We applied low‐temperature thermochronology and thermal modeling to study timing and drivers of cooling in the Patagonian Andes at the Chile triple junctionA Cretaceous cooling phase between 120 and 80 Ma was detected, directly linked to the first recorded Andean orogenic phase of the Patagonian AndesA 30‐10 Ma cooling phase is related to the main phase of crustal shortening during increased convergence prior to the collision of the Chile ridge; 7‐0 Ma cooling is likely linked to glaciations rather than to the development of slab window We applied low‐temperature thermochronology and thermal modeling to study timing and drivers of cooling in the Patagonian Andes at the Chile triple junction A Cretaceous cooling phase between 120 and 80 Ma was detected, directly linked to the first recorded Andean orogenic phase of the Patagonian Andes A 30‐10 Ma cooling phase is related to the main phase of crustal shortening during increased convergence prior to the collision of the Chile ridge; 7‐0 Ma cooling is likely linked to glaciations rather than to the development of slab window