Reconstructions of primary productivity at low latitudes have been the focus of several studies to better understand how the export of nutrient-rich, intermediate Southern Ocean (SO) waters influences productivity at these latitudes. This was triggered by the general observation of minima in the planktonic foraminiferal d13C values during deglaciations, which was interpreted as an isotopic signal of intermediate SO waters, together with concomitant increase in diatom productivity at some equatorial sites. However, the impact of these SO waters on productivity at higher latitudes is not well constrained. Here, we compare a high-resolution planktonic foraminiferal d13C record with total organic carbon and biomarker records for Proboscia diatoms and haptophytes from a core offshore Southeastern Australia (SEA). This shows that SEA received intermediate SO waters during deglaciations but it did not result in increased productivity during these periods. Instead, the highest primary productivity period, as shown by total organic carbon and alkenone accumulation rates, was during Last Glacial Maximum while Proboscia diatoms mainly proliferated during interglacials and Marine Isotope Stage 3, matching periods of increased diatom productivity in some sites of the Eastern Equatorial Pacific. Our study suggests that increased primary productivity offshore SEA is mainly due to stronger westerlies winds during glacial while Proboscia diatom productivity is likely to be also controlled by the transport of silicic acid to this area.