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Abstract Early Pleistocene Marine Isotope Stage (MIS)‐31 (1.081–1.062 Ma) is a unique interval of extreme global warming, including evidence of a West Antarctic Ice Sheet (WAIS) collapse. Here we present a new 1,000‐year resolution, spanning 1.110–1.030 Ma, diatom‐based reconstruction of primary productivity, relative sea surface temperature changes, sea‐ice proximity/open ocean conditions and diatom species absolute abundances during MIS‐31, from the Scotia Sea (59°S) using deep‐sea sediments collected during International Ocean Discovery Program (IODP) Expedition 382. The lower Jaramillo magnetic reversal (base of C1r.1n, 1.071 Ma) provides a robust and independent time‐stratigraphic marker to correlate records from other drill cores in the Antarctic Zone of the Southern Ocean (AZSO). An increase in open ocean speciesFragilariopsis kerguelensisin early MIS‐31 at 53°S (Ocean Drilling Program Site 1,094) correlates with increased obliquity forcing, whereas at 59°S (IODP Site U1537; this study) three progressively increasing, successive peaks in the relative abundance ofF. kerguelensiscorrelate with Southern Hemisphere‐phased precession pacing. These observations reveal a complex pattern of ocean temperature change and sustained sea surface temperature increase lasting longer than a precession cycle within the Atlantic sector of the AZSO. Timing of an inferred WAIS collapse is consistent with delayed warmth (possibly driven by sea‐ice dynamics) in the southern AZSO, supporting models that indicate WAIS sensitivity to local sub‐ice shelf melting. Anthropogenically enhanced impingement of relatively warm water beneath the ice shelves today highlights the importance of understanding dynamic responses of the WAIS during MIS‐31, a warmer than Holocene interglacial.