Reconstructions of ecosystem dynamics in tropical East Africa during the latest Pleistocene and the Holocene provide important long-term ecological insights, but so far, only a few, sometimes incomplete terrestrial records exist. In this paper, we present a new high-resolution palynological record from the Lake Victoria basin, covering the period from 16,600 to 9000 cal yr BP, when Afromontane forests and tropical rainforests gradually replaced the savanna. We discuss this dataset in the context of published palaeoclimate data, TEX86 inferred temperature and δD leaf wax inferred precipitation records, to assess long-term ecological successions and their potential causes. By ca. 16,500 cal yr BP, the movement of the Afrotropical rainbelt, not only brought an increase in temperature and moisture into the Lake Victoria basin, but also promoted the spread of arboreal taxa, such as Celtis and Podocarpus, at the expense of the savanna. At that time, fires were prominent in the sparse Afromontane vegetation. Later from ca. 15,500–15,000 cal yr BP, temperature and humidity rose and Afromontane trees such as Olea and Macaranga spread slightly, while grasses were burning in the savanna. During the period from 13,250 to 10,700 cal yr BP, Afromontane vegetation dominated by Olea became more prominent and expanded towards the lowlands where the tropical rainforest or gallery forest established; however, the savanna only marginally retreated. An initial spread of tropical rainforests occurred from ca. 11,500–11,100 cal yr BP during the onset of the Holocene, when temperatures and moisture further increased. Subsequently, between 10,700 and 10,300 cal yr BP the tropical savanna was largely replaced by the tropical rainforest, while the Afromontane forest likely spread to higher elevations, similar to the patterns observed today. Our high-resolution record demonstrates the dynamic response of African tropical ecosystems to major temperature and humidity variations from 16,600 to 9000 cal yr BP, including some of the most important landscape transformations in East Africa in the past 20,000 years.