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U-Pb zircon geochronology and isotopic records have played an influential role in our understanding of convergent margin dynamics. Orogenic cyclicity models link tectonic regimes with magmatic isotopic signatures in advancing orogens, relating compressional regimes with evolved signatures and extension with juvenile signatures; however, such frameworks may not apply for retreating orogens, which commonly produce substantial crustal heterogeneities during backarc rifting and ocean spreading. We explore the Mesozoic to Cenozoic Patagonian Andes tectonic evolution, combining U-Pb zircon ages, bulk rock εNd, and new detrital zircon εHf from the retroarc basin to understand the associated magmatic arc evolution during retreat and advance of the margin. Our results reveal a protracted phase of isotopically juvenile magmatism between 150 and 80 Ma, which began during backarc extension and persisted long after the margin switched to a contractional regime. We propose that the prolonged juvenile isotopic trend started mainly due to trenchward migration of the arc during backarc extension (150−120 Ma) and persisted due to partial melting of underthrusted juvenile attenuated and oceanic crust during backarc basin closure (120−80 Ma). This interpretation implies that tectonic stress alone does not predict isotopic trends, and factors like assimilation or the composition of underthrusted crust are important controls on magmatic isotopic composition, especially in retreating and transitional orogens.