Cenozoic growth of the Andes has been strongly influenced by subduction dynamics, reactivation of inherited crustal heterogeneities, and the superposed effects of climate. Subduction of the submarine Carnegie Ridge has fundamentally impacted late Cenozoic magmatism and tectonic activity in the northern Andes. Time-temperature inverse modeling of new thermochronological data from the Western Cordillera of Ecuador reveals two phases of cooling separated by isothermal conditions. The first cooling phase immediately postdates early and middle Miocene magmatism in the Western Cordillera and is attributed to post-magmatic thermal relaxation. The second cooling phase started after 6 Ma, which we infer to record the exhumation in the Western Cordillera, coeval with the last cooling phase in the Eastern Cordillera. Based on these findings we posit that the onset of subduction of the Carnegie Ridge at ~6-5 Ma increased plate coupling at the subduction interface and promoted shortening and regional rock uplift in the northern Andes. Overall, our results highlight the essential role of bathymetric anomalies in driving regional upper-plate deformation at non-collisional convergent plate margins.