The habitability and ecology of Earth is fundamentally shaped by surface temperature, but the temperature history of our planet is not easily reconstructed, especially before the evolution of early biomineralizing animals. This work presents a billion-year-long, high-resolution, mineral-specific record of oxygen isotope measurements in shallow marine rocks. Clumped isotope paleothermometry results from four minerals resolves previous ambiguity in seawater oxygen isotope composition and confirms that long-term cooling punctuated by short-lived temperature extremes are dominant components of this record. We consider post-depositional effects by comparing Phanerozoic rock and fossil records, and identify temporal and spatial controls on alteration. Furthermore, this record is suggestive of key differences in dolomite (CaMg(CO3)2) formation processes between the Neoproterozoic (1000–538.8 Ma) and Phanerozoic (538.8–0 Ma), consistent with previous suggestions based on petrographic and sedimentological observations. This record, when viewed alongside the fossil record, suggests temperature change is tightly coupled to extinction and origination in the history of life and carbon cycle perturbations over the last billion years.