Marine biological productivity has been invoked as a possible climate driver during the early Paleogene through its potential influence on atmospheric carbon dioxide concentrations. However, the relationship of export productivity (the flux of organic carbon (C) from the surface ocean to the deep ocean) to organic C burial flux (the flux of organic C from the deep ocean that is buried in marine sediments) is not well understood. We examine the various components involved with atmosphere-to-ocean C transfer by reconstructing early Paleogene carbonate and silica production (using carbonate and silica mass accumulation rates (MARs)); export productivity (using biogenic barium (bio-Ba) MARs); organic C burial flux (using reactive phosphorus (P) MARs); redox conditions (using uranium and manganese contents); and the fraction of organic C buried relative to export productivity (using reactive P to bio-Ba ratios). Our investigations concentrate on Paleocene/Eocene sections of Sites 689/690 from Maud Rise and Site 738 from Kerguelen Plateau. In both regions, export productivity, organic C burial flux, and the fraction of organic C buried relative to export productivity decreased from the Paleocene/early Eocene to the middle Eocene. A shift is indicated from an early Paleogene two-gyre circulation in which nutrients were not efficiently recycled to the surface via upwelling in these regions, to a circulation more like the present day with efficient recycling of nutrients to the surface ocean. Export productivity was enhanced for Kerguelen Plateau relative to Maud Rise throughout the early Paleogene, possibly due to internal waves generated by the plateau regardless of gyre circulation.