The subduction of bathymetric highs, such as aseismic ridges, leads to far‐reaching changes in the dynamics of subduction zones with increased plate coupling and deformation in the upper plate. Subduction of the submarine Carnegie Ridge on the Nazca Plate has fundamentally impacted late Cenozoic magmatism and tectonic activity in the northern Andes. However, the timing of onset of Carnegie Ridge subduction has been a matter of debate. 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 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. Inferred to record the onset of tectonically controlled rock uplift and exhumation in the Western Cordillera, this phase is coeval with the last cooling phase recorded in the Eastern Cordillera. Based on these findings, we suggest that the onset of subduction of the Carnegie Ridge at ∼6–5 Ma increased plate coupling at the subduction interface, promoting shortening, regional rock uplift, and exhumation in the northern Andes. Overall, our results highlight the essential role of bathymetric highs in driving regional upper‐plate deformation at non‐collisional convergent plate margins.