During Marine Isotope Stage 3 (MIS-3; 57–29 ka) Antarctic ice cores reveal a glacial climate state punctuated by millennial-scale warming events and pulses of CO₂. Changes in iron-fertilised export production and ocean circulation/upwelling, interpreted from South Atlantic sediment cores, suggest that the Southern Ocean is a conduit for the storage and release of CO₂ from the deep ocean. However, it is unclear whether this occurs throughout the Southern Ocean as these processes have not previously been investigated in the southwest Pacific . Here we describe localised iron limitation linked to glaciation changes in New Zealand, which reduced export production during early MIS-3 (60–48 ka) and caused decreases/increases in export production during late MIS-3 (48–29 ka) millennial-scale warming/cooling. Consistent decreases in foraminifera-bound δ¹⁵N during all MIS-3 warming events may reflect changes in the supply of nitrate to the subantarctic Pacific, possibly from increased wind-driven upwelling in the Antarctic and northward eddy-driven transport and/or shifting SO fronts. Concomitant decreases in bottom water oxygen and increases in the ¹⁴C age of deep waters suggest that old, nutrient-rich waters influenced upper circumpolar deep water in the southwest Pacific during warming events. This signature may reflect an expansion of Pacific Deep Water into the Southern Ocean as Southern Ocean overturning strengthens. Iron-limitation of export production, the expansion of Pacific Deep water, and increased wind-driven upwelling would all work to contribute to increasing atmospheric CO₂ through reduced drawdown, and increased outgassing from the Pacific carbon reservoir during the millennial-scale warming events of MIS-3.