São Tomé (Gulf of Guinea, Central Africa) is a 854 km2 tropical island that had a pivotal role in early European colonial expansion through the Atlantic between the 15th and 16th centuries. Historical sources suggest that native vegetation has been heavily impacted since human arrival (1470 CE) due to monoculture economies and the introduction of mammals and plants, some of which now have established wild populations. The Afromontane forest of São Tomé, located above 800 m.a.sl., is particularly rich in endemic plant species and has remained relatively unaffected by direct human impacts. Here, we explore how environmental change influenced this forest through the study of a sedimentary sequence from the volcanic crater of Lagoa Amélia (1340 m a.s.l.), a palustrine system located at the boundary between submontane (800-1400 m a.s.l.) and mist forest (above 1400 m a.s.l.). We used fossil pollen, non-pollen palynomorphs, sedimentology and charcoal to determine forest dynamics from the Late Pleistocene to the present. From 14,000 to 12,500 cal yr BP the forest was dominated by taxa from higher altitudes, adapted to cooler and drier climates (e.g. Afrocarpus mannii trees and Psychotria nubicola). After 12,500 cal yr BP, a potential uphill migration was identified by an increase in taxa like the trees Symphonia globulifera and Craterispermum cerinanthum. From 11,200 cal yr BP through the rest of the Holocene taxa from lower altitudes became dominant (e.g. Prunus africana, Polyscias, and Sabicea), except at c. 8500 cal yr BP when rapid cooling led to forest opening. Charcoal showed that fires were frequent during the Late Pleistocene (14,000 to 11,200 cal yr BP), becoming rare during the Holocene until anthropogenic fires started at c. 220 cal yr BP. Other recent anthropogenic impacts detected in Lagoa Amélia included the appearance of pollen of introduced plant species (e.g., Cestrum), and the increase in pollen of economically important species (Elaeis guineensis, Zea mays) and in fungal spores related to introduced herbivores. Our results reveal that climate changed the altitudinal distribution of the Afromontane forest in São Tomé during the Late Pleistocene, as observed on the African continent, and that this ecosystem was also strongly impacted by human arrival, through fire, farming, and introduced species.