The remarkable correspondence between glacial-interglacial changes in atmospheric CO2 levels and global climate over much of the Pleistocene suggests that CO2 is also a key climate change driver. However, there is as yet no widely accepted explanation of the low glacial CO2 levels. Here I use an intermediate-complexity climate model to show that glacial cooling, acting on the rates of organic carbon production and decay in the ocean, can explain a significant portion of the glacial CO2 lowering. New model results show that cooling strengthens the vertical transport of organic carbon from the surface ocean to the deep ocean, reduces atmospheric pCO2, and shifts nutrients from the Atlantic basin to the Indo-Pacific basins. The overall vertical transport is increased because the cooling effect on reducing the degradation rate of sinking particulate organic carbon is greater than on reducing the export production. This net temperature effect on atmospheric pCO2 mediated by biology is comparable to the temperature effect on atmospheric pCO2 driven by solubility, which is almost always mentioned as a large factor in the glacial CO2 levels. An implication for the future is that higher ocean temperatures will act as a positive feedback on atmospheric CO2 by reducing the vertical transport of carbon to the deep ocean and thereby increasing CO2 degassing from the ocean.