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‘The Blob’, a mass of anomalously warm water in the Northeast Pacific Ocean peaking from 2014 to 2016, caused a decrease in primary productivity with cascading effects on the marine ecosystem. Among the more obvious manifestations of the event were seabird breeding failures and mass mortality events. Here, we used corticosterone in breast feathers (fCort), grown in the winter period during migration, as an indicator of nutritional stress to investigate the impact of the Blob on two sentinel Pacific auk species (family Alcidae). Feathers were collected from breeding females over 8 years from 2010 to 2017, encompassing the Blob period. Since Pacific auks replace body feathers at sea during the migratory period, measures of fCort provide an accumulated measure of nutritional stress or allostatic load during this time. Changes in diet were also measured using δ15N and δ13C values from feathers. Relative to years prior to the Blob, the primarily zooplanktivorous Cassin’s auklets (Ptychoramphus aleuticus) had elevated fCort in 2014–2017, which correlated with the occurrence of the Blob and a recovery period afterwards, with relatively stable feather isotope values. In contrast, generalist rhinoceros auklets (Cerorhinca monocerata) displayed stable fCort values across years and increased δ15N values during the Blob. As marine heatwaves increase in intensity and frequency due to climate change, this study provides insight into the variable response of Pacific auks to such phenomena and suggests a means for monitoring population-level responses to climatological variation.