The Antarctic Cold Reversal (ACR; 14.7 to 13 ka) phase of the last deglaciation saw a pause in the rise of atmospheric pCO2 and Antarctic temperature, contrasted with warming in the North. Mechanisms associated with interhemispheric heat transfer have been proposed to explain features of this event, but the response of marine biota and the carbon cycle are debated. The Southern Ocean is a key site of deep-water exchange with the atmosphere, hence deglacial changes in nutrient cycling, circulation, and productivity in this region may have global impact. Here we present a new perspective on the sequence of events in the deglacial Southern Ocean, that includes multi-faunal benthic assemblage (foraminifera and cold-water corals) and geochemical data (Ba/Ca, 14C, δ11B) from the Drake Passage. Our records feature anomalies during peak ACR conditions indicative of circulation, biogeochemistry, and regional ecosystem perturbations. Within this cold episode, peak abundances of thick-walled benthic foraminifera and cold-water corals are observed at shallow depths in the sub-Antarctic (~300 m), while coral populations at greater depths and further south diminished. Geochemical data indicate that habitat shifts were associated with enhanced primary productivity in the sub-Antarctic, a more stratified water column, and poorly oxygenated bottom water. These results are consistent with northward migration of primary production in response to Antarctic cooling and widespread biotic turnover across the Southern Ocean. We suggest that expanding sea ice, suppressed ventilation, and shifting centres of upwelling drove changes in planktic and benthic ecology, and were collectively instrumental in halting CO2 rise in the mid-deglaciation.