The Southern Ocean plays a crucial role in the global carbon budget. One key interval for understanding this role is the Antarctic Cold Reversal (14,700–12,700 calibrated (cal) yr BP)—a Southern Hemisphere-specific cooling event that temporarily reversed the deglacial trend of warming and rising atmospheric CO₂. Modelling studies propose that the atmospheric CO₂ plateau during the Antarctic Cold Reversal is related to increased marine productivity. However, proxy constraints on the primary producer community are limited to the subset of groups that leave a fossil record. Here we applied ancient DNA shotgun metagenomics to samples from a marine sediment core to characterize the composition of the marine ecosystem across all trophic levels, finding that the haptophyte algae Phaeocystis antarctica was the dominant primary producer during the event. Independent proxy evidence from the same record points to high productivity in response to enhanced sea-ice seasonality caused by the cooling. Post Antarctic Cold Reversal, abrupt Phaeocystis community loss shows how sensitive this ecosystem is to warming, potentially representing a key tipping element. As an analogy for present warming, it highlights the importance of regions with high seasonal sea-ice variability and Phaeocystis dominance, such as the Ross Sea, in stabilizing atmospheric CO₂ content.