Over the last deglaciation there were two transient intervals of pronounced atmospheric CO2 rise; Heinrich Stadial 1 (17.5-15 kyr) and the Younger Dryas (12.9-11.5 kyr). Leading hypotheses accounting for the increased accumulation of CO2 in the atmosphere at these times invoke deep ocean carbon being released from the Southern Ocean and an associated decline in the global efficiency of the biological carbon pump. Here we present new deglacial surface seawater pH and CO2sw records from the Sub-Antarctic regions of the Atlantic and Pacific oceans using boron isotopes measured on the planktic foraminifera Globigerina bulloides. These new data support the hypothesis that upwelling of carbon-rich water in the Sub-Antarctic occurred during Heinrich Stadial 1, and contributed to the initial increase in atmospheric CO2. The increase in CO2sw is coeval with a decline in biological productivity at both the Sub-Antarctic Atlantic and Pacific sites. However, there is no evidence for a significant outgassing of deep ocean carbon from the Sub-Antarctic during the rest of the deglacial, including the second period of atmospheric CO2 rise coeval with the Younger Dryas. This suggests that the second rapid increase in atmospheric CO2 is driven by processes operating elsewhere in the Southern Ocean, or another region.