Understanding the Earth’s climate system during past periods of high atmospheric CO₂ is crucial for forecasting climate change under anthropogenically-elevated CO₂. The Mesozoic Era is believed to have coincided with a long-term Greenhouse climate, and many of our temperature reconstructions come from stable isotopes of marine biotic calcite, in particular from belemnites, an extinct group of molluscs with carbonate hard-parts. Yet, temperatures reconstructed from the oxygen isotope composition of belemnites are consistently colder than those derived from other temperature proxies, leading to large uncertainties around Mesozoic sea temperatures. Here we apply clumped isotope palaeothermometry to two distinct carbonate phases from exceptionally well-preserved belemnites in order to constrain their living habitat, and improve temperature reconstructions based on stable oxygen isotopes. We show that belemnites precipitated both aragonite and calcite in warm, open ocean surface waters, and demonstrate how previous low estimates of belemnite calcification temperatures has led to widespread underestimation of Mesozoic sea temperatures by ca. 12 °C, raising estimates of some of the lowest temperature estimates for the Jurassic period to values which approach modern mid-latitude sea surface temperatures. Our findings enable accurate recalculation of global Mesozoic belemnite temperatures, and will thus improve our understanding of Greenhouse climate dynamics.