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Abstract The last deglaciation (~20–10 kyr BP) was characterized by a major shift in Earth's climate state, when the global mean surface temperature rose ~4 °C and the concentration of atmospheric CO₂increased ~80 ppmv. Model simulations suggest that the initial 30 ppmv rise in atmospheric CO₂may have been driven by reduced efficiency of the biological pump or enhanced upwelling of carbon‐rich waters from the abyssal ocean. Here we evaluate these hypotheses using benthic foraminiferal B/Ca (a proxy for deep water [CO₃²⁻]) from a core collected at 1,100‐m water depth in the Southwest Atlantic. Our results imply that [CO₃²⁻] increased by 22 ± 2 μmol/kg early in Heinrich Stadial 1, or a decrease in ΣCO₂of approximately 40 μmol/kg, assuming there were no significant changes in alkalinity. Our data imply that remineralized phosphate declined by approximately 0.3 μmol/kg during Heinrich Stadial 1, equivalent to 40% of the modern remineralized signal at this location. Because tracer inversion results indicate remineralized phosphate at the core site reflects the integrated effect of export production in the sub‐Antarctic, our results imply that biological productivity in the Atlantic sector of the Southern Ocean was reduced early in the deglaciation, contributing to the initial rise in atmospheric CO₂.