Changes in ocean circulation and the biological carbon pump have been implicated as the drivers behind the rise in atmospheric CO2 across the last deglaciation; however, the processes involved remain uncertain. Previous records have hinted at a partitioning of deep ocean ventilation across the two major intervals of atmospheric CO2 rise, but the consequences of differential ventilation on the Si cycle has not been explored. Here we present three new records of silicon isotopes in diatoms and sponges from the Southern Ocean that together show increased Si supply from deep mixing during the deglaciation with a maximum during the Younger Dryas (YD). We suggest Antarctic sea ice and Atlantic overturning conditions favoured abyssal ocean ventilation at the YD and marked an interval of Si cycle reorganisation. By regulating the strength of the biological pump, the glacial–interglacial shift in the Si cycle may present an important control on Pleistocene CO2 concentrations.