Calcareous nannofossil assemblages and fragmentation ratios of two coccolithophore species (Coccolithus pelagicus and Calcidiscus leptoporus) were analysed in samples from ODP Site 1090, South Atlantic (42° 54.8′S, 8° 53.9′E), to obtain valuable insights into the paleoceanographic evolution and carbonate preservation trends during the late Pliocene and Early Pleistocene (3.14–1.80 Ma). Coccolithophore species were identified in a total of 232 samples. Calcareous nannofossil counts revealed shifts in the assemblages that can be correlated with the climatic evolution of the Southern Ocean. Between 3.2 and 2.85 Ma, i.e. during the mid-Pliocene Warmth, the assemblage was dominated by small Gephyrocapsa, a group of species typically associated with upwelling conditions. The dominance of the opportunistic small Gephyrocapsa group can be linked to a more intense mixing of the upper water column most likely due to the more southward position of the Subtropical Front (STF) compared with its present position. After 2.85 Ma, a gradual increase in the cold water species C. pelagicus marked a progressive cooling of the South Atlantic coupled with a northward shift of the (STF). The changes in the assemblage composition co-varied with the δ18O record. Periods with isotopically heavier values (glacial) were dominated by C. pelagicus and periods with lighter values (interglacial) were dominated by very small reticulofenestrids (VSR; <3 μm). After 2.7 Ma, an intensification of the glacial-interglacial patterns of C. pelagicus and VSR was registered. The interval between 2.44 and 2.34 Ma was characterised by low abundance of C. pelagicus and higher biodiversity which are interpreted to be due to a temporal southward movement of the STF interrupting the previously registered cooling. After 2.0 Ma, the decreasing abundance of C. pelagicus suggests a slowdown of the relatively intense cooling registered since 2.7 Ma. The fragmentation ratios of C. pelagicus and C. leptoporus suggest moderate preservation along our interval, with a general trend toward better preservation after 2.2 Ma. This enhanced preservation has been related to a greater input of the less-corrosive northern component water mass into the Cape Basin after 2.2 Ma. The lack of significant glacial-interglacial variations in the fragmentation ratios suggests that the low amplitude of the glacial cycles did not have a substantial impact on the carbonate preservation throughout the entire interval. During MIS 99–98 (approximately 2.5 Ma), a remarkably high accumulation of VSR was found and identified as a short (9 ka) event of high productivity. The timing of this event coincides with that of the Eltanin impact (approximately 2.5 Ma), suggesting that, albeit speculatively, the two events may be related.