Antarctic Bottom Water formation, such as in the Weddell Sea, is an efficient vector for carbon sequestration on time scales of centuries. Yet, possible changes in carbon sequestration under changing environmental conditions are unquantified to date, mainly due to difficulties in simulating the relevant processes on high-latitude continental shelves. Using a model setup including both ice-shelf cavities and oceanic carbon cycling, we demonstrate that by 2100, deep-ocean carbon accumulation in the southern Weddell Sea is abruptly attenuated to only 40% of the rate in the 1990s in a high-emission scenario, while still being 4-fold higher in the 2080s. By assessing deep-ocean carbon budgets and water mass transformations, we show that this decline can be attributed to an increased presence of Warm Deep Water on the southern Weddell Sea continental shelf, a 16% reduction in sea-ice formation, and a 79% increase in ice-shelf basal melt. Altogether, these changes lower the density and volume of newly formed bottom waters and reduce the associated carbon transport to the abyss.