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Abstract Understanding the mechanism of selective extinction is important in predicting the impact of anthropogenic environmental changes on current ecosystems. The selective extinction of externally shelled cephalopods at the Cretaceous-Paleogene (K-Pg) mass extinction event (ammonoids versus nautiloids) is often studied, but its mechanism is still debated. We investigate the differences in metabolic rate between these two groups to further explore the causes of selective extinction. We use a novel metabolic proxy—the fraction of metabolic carbon in the stable carbon isotope ratio of shell material (Cmeta)—to determine metabolic rate. Using this approach, we document significant differences in Cmeta among modern cephalopod taxa (Nautilus spp., Argonauta argo, Dosidicus gigas, Sepia officinalis, and Spirula spirula). Our results are consistent with estimates based on oxygen consumption, suggesting that this proxy is a reliable indicator of metabolic rate. We then use this approach to determine the metabolic rates of ammonoids and nautiloids that lived at the end of the Cretaceous (Maastrichtian). Our results show that the nautiloid Eutrephoceras, which survived the K-Pg mass extinction event, possessed a lower metabolic rate than co-occurring ammonoids (Baculites, Eubaculites, Discoscaphites, and Hoploscaphites). We conclude that the lower metabolic rate in nautiloids was an advantage during a time of environmental deterioration (surface-water acidification and resulting decrease in plankton) following the Chicxulub asteroid impact.