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Abstract Lithospheric foundering is an important mechanism of crustal deformation and recycling, basin subsidence, and surface uplift in orogenic systems. The Arizaro Basin, in the Puna region of NW Argentina, is a place where foundering was proposed to have taken place during the late Miocene. The Arizaro Basin has been described as a “bobber” basin produced by Miocene lithospheric foundering. The geometry, sedimentology, deformation, and paleoelevation history of the Arizaro Basin and surrounding arc suggest dynamic processes associated with lithospheric removal. Although analogue and numerical models support this hypothesis, the history of crustal thickness in response to lithospheric removal remains unconstrained. Here, we used a novel approach exploiting the geochemistry of detrital zircons from volcanic ashes intercalated within the Arizaro Basin stratigraphy to reconstruct the paleocrustal thickness of the neighboring magmatic sources throughout the Cenozoic. Our data indicate that the sources of volcanism for the Arizaro Basin were characterized by relatively thick crust (~53 km) since ca. 36 Ma. Thickening between ca. 20 and 13 Ma and thinning after ca. 13 Ma are consistent with formation and subsequent removal of a crustal root under the nearby arc and Aguas Calientes caldera.