AbstractStudies of Antarctic paleo‐archives have produced conflicting hypotheses on the relative impact of long‐term climate change and historic exploitation of marine mammals on Southern Ocean krill predator foraging ecology. We disentangle these hypotheses using amino acid stable isotope analysis on a 7000‐yr Holocene archive of Adélie penguin (Pygoscelis adeliae) eggshells to differentiate variation in diet and trophic dynamics from baseline biogeochemical cycling as drivers of the rapid decline in krill predator bulk tissue δ15N values in recent centuries. Contrary to previous hypotheses suggesting solely trophic dynamic mechanisms as drivers of this decline, we identified an abrupt decline in source amino acid δ15N values, indicative of major changes in biogeochemical cycling at the base of the Southern Ocean food web that mirrored the decline in penguin bulk tissue δ15N values. These abrupt shifts in penguin δ15N values and associated biogeochemical cycling aligned with climatic events during the Little Ice Age that decreased surface δ15NNO3−, likely connected to a proposed increase in Ekman upwelling via a southward migration of the Westerlies. This baseline shift was in addition to a long‐term, gradual decline in penguin trophic position over the Holocene that began prior to both recent anthropogenic climate change and a proposed “krill‐surplus” following historic marine mammal exploitation in the 19th and 20th centuries. In resolving these outstanding hypotheses about drivers of Southern Ocean food web dynamics, this study emphasizes the fundamental importance of climate‐induced variability in biogeochemical cycling on ecological processes and improves the ability of paleo‐archives to inform the ecological consequences of future environmental change in the Southern Ocean.