The Southern Ocean is a key region for climate changes, notably for deep ocean–atmosphere CO2 exchange, linked to the upwelling of deep waters, south to the Polar Front, that is driven through Southern Hemisphere Westerly Winds and Antarctic Circumpolar Current positions and intensities. Previous studies using a range of different proxies have proposed the latitudinal migration of the Antarctic Circumpolar Current and Southern Westerly Winds in the Southeast Pacific since the Last Glacial Maximum, but with conflicting results. We present a paleoceanographic reconstruction from the Last Glacial period to the Late Holocene based on diatom and foraminiferal assemblages from the marine sediment core MD07-3081, retrieved from the Southeast Pacific at 49° S, proximal (∼100 km) offshore the south coast of Chile. During the Last Glacial, the presence of polar diatoms is not observed, suggesting that the Polar Front did not approach 49° S. During the deglaciation, an increase of Chaetoceros spp. spores is observed together with the opportunistic planktonic foraminifer Globigerinita glutinata, which indicates a greater nutrient availability, linked to the influence of the Southern Ocean upwelling. The presence of Neogloboquadrina incompta, a subtropical species, during two periods of the deglaciation (15.2 ka and 12.3–11.5 ka) is associated with a southward shift of the Subtropical Front linked to a reduction of the South Pacific split jet. During the deglaciation to the Early Holocene transition, the increase of open ocean diatoms thriving both north and south of the Subantarctic Zone indicates a greater influence of the Antarctic Circumpolar Current, possibly displaced ∼3° south of its current position at 46° S. In the Late Holocene, the increase of subtropical-temperate species, e.g. Fragilariopsis doliolus, is indicative of a greater influence of warm waters coming from the Peru–Chile Countercurrent. This study of the diatom and foraminiferal assemblages provide new insights into the paleoceanography of the SE Pacific since the Last Glacial Maximum and the role of the Southern Ocean during this climate transition.