In the Southern Ocean (SO), climate-driven latitudinal migrations of the Antarctic Circumpolar Current (ACC) frontal system impact large-scale ocean circulation and primary productivity. Latitudinal migrations may not have been identical in all SO basins due to the presence or absence of regional bathymetric obstacles. The Antarctic Polar Front (APF), defined by the 3–5 °C surface temperature range and the 2 °C subsurface temperature minimum at 200 m, is particularly important for nutrient redistribution and biodiversity, influencing the soft tissue carbon pump in the modern SO. However, previous assessments of its migrations in the past, mostly based on a single metric or indirect observations, were not always robust. Here, we combine a new proxy for subsurface temperature (sub-ST) reconstructions based on radiolarian assemblages (sub-STrad), with relative abundance variations of key radiolarian species, and sea-surface temperatures (SST) reconstructions, based on diatom assemblages (SSTdiat), to refine estimations of the past mean APF locations in the Kerguelen Plateau (KP) region. Data from three sediment cores on a south (55°S) to north (47°S) transect are used to trace the mean APF locations for three climate states, glacials, peak-interglacials and mild-interglacials. Our results suggest that the APF, presently located south of Kerguelen Islands, shifted by 6–7 degrees of latitude and was located north of the KP during all glacial periods of the last 360 kyrs. This suggests that the ACC major flow interacted less with the bottom topography relative to its modern counterpart, probably resulting in less mixing of the water column over and in the lee of the KP. We propose that this process participated in the isolation of Antarctic surface waters (AASW) and in the reduction of macro-nutrient supply, thus resulting in lower regional productivity. During the warmer-than-present early interglacial periods, the APF probably migrated south by ~5 degrees of latitude relative to its modern position, to pass through the Fawn Trough. Contrary to glacial periods, the APF was forced in an “S” shape while the ACC main flow was constrained against the northern tip of the KP. In this configuration, a stronger interaction between the ACC, its associated fronts, and topography is expected, resulting in more mixing of the water column over and east of the KP. Congruently, siliceous productivity was probably restrained to latitudes south of the Fawn Trough.