Ocean chemistry is affected by pCO₂ in the atmosphere by increasing the dissolution of solid calcium carbonate and elevating the dissolved inorganic carbon concentrations in seawater. Positive feedbacks between the ocean and atmosphere can maintain high atmospheric pCO₂ and affect global climate. We report evidence for changes in the oceanic carbon cycle from the first high-quality organic carbon (C_org) data set of Eocene sediments beneath the equatorial Pacific upwelling region (Leg 199 of the Ocean Drilling Program). Eocene C_org mass accumulation rates (MARs) are 10 times lower than Holocene rates, even though expected C_org MARs estimated from biogenic-barium MARs (an indicator of biological production) equal or exceed modern fluxes. What happened to the missing C_org? Recent advances in ecology and biochemical kinetics show that the metabolism of nearly all animals, marine and terrestrial, is positively correlated by first principles to environmental temperatures. The approximately 10°C abyssal temperature difference from Eocene to Holocene should have radically reduced pelagic C_org burial, as we observe. We propose that higher basal metabolism and nutrient utilization/recycling rates in the Eocene water column and surface sediments precluded C_org sediment burial in the pelagic ocean. Increased rates of metabolism, nutrient utilization, and lowered C_org sedimentation caused by increased temperature may have acted as a biological feedback to maintain high atmospheric pCO₂ and hothouse climates. Conversely, these same parameters would reverse sign to maintain low pCO₂ when temperatures decrease, thereby maintaining “icehouse” conditions during cold climate regimes.