Tropical mountain ecosystems hold immense ecological and economic importance, yet they face disproportionate risks from shifting tropical climates. For example, present-day montane vegetation of East Africa is characterized by different plant species that grow in and are restricted to certain elevations due to environmental tolerances. As climate changes and temperature/rainfall zones move on mountains, these species must rapidly adjust their ranges or risk extinction.Paleoenvironmental records offer valuable insights into past climate and ecosystem dynamics, aiding predictions for ongoing climate change impacts. In particular, warming and wetting in tropical East Africa during the mid-Holocene resulted in both lowland and highland forest expansion. However, the relative impacts of rainfall and temperature change on montane ecosystems along with the influence of lowland forest expansion on montane communities is not completely understood. We use fossil pollen to study the vegetation changes in two lakes at different altitudes in the Rwenzori Mountains, Uganda: Lake Mahoma (Montane Forest belt) and Upper Kachope Lake (Afroalpine belt). Further, using the newly relaunched African Pollen Database and recent temperature reconstructions, we provide a regional synthesis of vegetation changes in the Rwenzori and then compare this with changes observed from other equatorial East African montane sites (particularly Mt Kenya).In the early to mid-Holocene in the Rwenzori Mountains, trees common today in lowland forests dominated, driven largely by warmer temperatures. After 4000 years ago (4ka), Afromontane forest trees along with grasses progressively replaced lowland trees. Not all sites experienced identical transitions. For instance, at Lake Rutundu on Mt Kenya at the same elevation as Lake Mahoma, bamboo expansion preceded Afromontane forest growth, likely influenced by variations in fire. Variance partitioning indicates that each site responded differently to changes in temperature and rainfall. Therefore, these site-specific ecological responses underscore the importance of considering biogeographic legacies as management strategies are developed, despite similarities in modern ecology.