Vertical migrations by marine organisms contribute to carbon export by consumption of surface phytoplankton followed by defecation in the deep ocean. However, biogeochemical models lack observational data, leading to oversimplified representation of carbon cycling by migrating organisms, such as Antarctic krill (Euphausia superba). Using a numerical model informed by 1 year of acoustic observations in the East Antarctic, we estimated the total particulate organic carbon (POC) flux from krill fecal pellets to be 9.68 milligrams of carbon per square meter per day (mg C m-2 day-1). A maximum of 25% of krill migrated to depths >200 m with a strong seasonality component, transporting <10% of the total krill POC flux (1.28 mg C m-2 day-1) to the deep ocean. Accurate carbon flux estimates are essential to inform climate policy and mitigation strategies, and models that include vertical migration will overestimate carbon export if this seasonality is not captured.