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Marine plankton have been conspicuously affected by recent climate change, responding with profound spatial relocations and shifts in the timing of their seasonal occurrence. These changes directly affect the global carbon cycle by altering the transport of organic material from the surface ocean to depth, with consequences that remain poorly understood. We investigated how distributional and abundance changes of copepods, the dominant group of zooplankton, have affected biogenic carbon cycling. We used trait-based, mechanistic models to estimate the magnitude of carbon transported downward through sinking faecal pellets, daily vertical migration and seasonal hibernation at depth. From such estimates for over 200,000 community observations in the northern North Atlantic we found carbon flux increased along the northwestern boundary of the study area and decreased in the open northern North Atlantic during the past 55 years. These changes in export were primarily associated with changes in copepod biomass, driven by shifting distributions of abundant, large-bodied species. Our findings highlight how recent climate change has affected downward carbon transport by altering copepod community structure and demonstrate how carbon fluxes through plankton communities can be mechanistically implemented in next-generation biogeochemical models with size-structured representations of zooplankton communities.