The Eocene-Oligocene transition (EOT) marks the onset of Antarctic glaciation at 33.7 Ma. Although the benthic oxygen isotope record defines the major continental ice sheet expansion, recent sedimentary and geochemical evidence suggests the presence of earlier ephemeral ice sheets. Sediment cores from Ocean Drilling Program Legs 119 and 188 in Prydz Bay provide an archive of conditions in a major drainage system of East Antarctica. We study biomarker and microfossil evidence to discern how the vegetation and climate shifted between 36 and 33 Ma. Pollen was dominated by reworked Permian Glossopterid gymnosperms; however, penecontemporaneous Eocene pollen assemblages indicate that some vegetation survived the glacial advances. At the EOT, brGDGT soil biomarkers indicate abrupt cooling from 13°C to 8°C and soil pH increases from 6.0 to 6.7, suggesting drying which is further supported by plant wax hydrogen and carbon isotopic shifts of 20‰ and 1.1‰, respectively, and evidence for drying from weathering proxies. Although the terrestrial soil biomarker influx mostly precludes the use of TEX86, we find sea surface temperatures of 12°C in the late Eocene cooling to 8°C at the EOT. Marine productivity undergoes a sustained increase after the glacial advance, likely promoted by enhanced ocean circulation. Between the two glacial surge events of the Priabonian Oxygen Maximum at 37.3 Ma and the EOT at 33.7 Ma, we observe warming of 2–5°C at 35.7 and 34.7 Ma, with increase in penecontemporaneous pollen and enhanced marine productivity, capturing the last flickers of Antarctic warmth.