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The impact of an asteroid at the end of the Cretaceous caused mass extinctions in the oceans. A rapid collapse in surface to deep-ocean carbon isotope gradients suggests that transfer of organic matter to the deep sea via the biological pump was severely perturbed. However, this view has been challenged by the survival of deep-sea benthic organisms dependent on surface-derived food and uncertainties regarding isotopic fractionation in planktic foraminifera used as tracers. Here we present new stable carbon (δ13C) and oxygen (δ18O) isotope data measured on carefully selected planktic and benthic foraminifera from an orbitally dated deep-sea sequence in the southeast Atlantic. Our approach is unique in that it combines δ18O evidence for habitat depth of foraminiferal tracer species with species-specific δ13C eco-adjustments, and compares isotopic patterns with corresponding benthic assemblage data. Our results show that changes in ocean circulation and foraminiferal vital effects contribute to but cannot explain all of the observed collapse in surface to deep-ocean foraminiferal δ13C gradient. We conclude that the biological pump was weakened as a consequence of marine extinctions, but less severely and for a shorter duration (maximum of 1.77 m.y.) than has previously been suggested.