We report the discovery of Archean (2980–2670 Ma) zircons from the Yilgarn Craton in Western Australia that record unusually low δ18O signatures (to –0.5‰). These zircons occur in cordierite-orthopyroxene granulites that retain the geochemical signature of intense pre-metamorphic hydrothermal alteration. We propose a model whereby the low-δ18O zircons crystallized within protoliths that record multiple stages of high-temperature interaction and hydrothermal exchange between shallow crustal material and 18O-depleted meteoric fluids, in a setting analogous to that of the Yellowstone caldera. Burial and subsequent granulite-facies metamorphism of this crust led to the crystallization of zircon, which acquired and preserved the extremely 18O-depleted signature of the whole rock. The apparent absence of strongly 18O-depleted Archean zircons has been a puzzling feature of the global zircon record, but we suggest this is an artifact of poor preservation potential. Our findings suggest that long-lived, shallow crustal magmatic-hydrothermal systems similar to those operating in modern caldera complexes were also a feature of Archean Earth.