The evolutionary history of lowland southern South American vegetation, particularly during the Paleocene−Eocene, remains enigmatic due to few existing paleobotanical records. Existing vegetation models present contradicting hypotheses ranging from expansive grasslands to tropical forests during this time. Resolving these contradictions is critical for reconstructing the ecological context surrounding the emergence of endemic South American faunas and understanding the relationship between climate and vegetation structure and composition during the warmest interval of the Cenozoic. Here, we present a basin-wide phytolith analysis from Paleocene−Eocene terrestrial deposits in the San Jorge Basin, Argentine Patagonia. These records expand existing phytolith studies and integrate new radiometric dates, providing a temporally resolved view of vegetation dynamics in the early Cenozoic. Phytolith assemblage composition suggests that forests dominated lowland ecosystems during the warm and humid Paleocene to the middle Eocene. Relative palm abundance increased between the middle and late Eocene as lowland humid megathermal forests began transitioning to progressively colder, arid, and more open vegetation, corroborated by existing paleobotanical, geochemical, and faunal records. Grasses were rare and likely represented forest understory elements until at least the early−middle Miocene, contradicting hypotheses of early Cenozoic grassy habitats in South America. Grass abundances increased between the early and middle Miocene alongside the return of humid forests as temperatures and precipitation rose in the region. Sustained cooling and aridification between the middle Miocene and the Quaternary led to the rise of Patagonian steppe vegetation.