Abstract The Choquequirao Formation is a >3 km-thick amphibolite-grade succession that outcrops in the Central Andes of southern Peru. To constrain its age and tectonostratigraphic setting, detrital zircon and metamorphic zircon, titanite, and rutile U–Pb isotopic analyses were conducted. Mantle-derived c. 640 Ma detrital zircons constrain the maximum age of the lower part of the succession and 550–490 Ma metamorphic zircon domains constrain its minimum age. The absence of early Paleozoic detrital zircons suggests that deposition predated early Paleozoic orogenesis in southwestern Gondwana. The close similarity of detrital zircon age spectra to those from sediments deposited on the Arequipa basement suggests that the Choquequirao Formation was deposited on the Arequipa Terrane. Metamorphic titanite dates are highly overdispersed, yet they overlap with c. 460 Ma peak metamorphism recorded by metamorphic zircon. Pb-loss pathways displayed by metamorphic titanite have a lower intercept that overlaps with c. 325 Ma metamorphic rutile, which corresponds to Hercynian orogenesis. A poorly constrained upper intercept of c. 510 Ma may correspond to Pampean and/or early Famatinian orogenesis. We interpret the Cryogenian–Ediacaran Choquequirao Formation as having been deposited during the opening of the Palaeo-Iapetus (Puncoviscana–Clymene) Ocean between eastern Arequipa and southern Kalahari prior to the subsequent collision with southwestern Amazonia during the Pampean Orogeny.