In Africa, the early Holocene was characterized by wetter, warmer conditions than today, followed by rapid aridification at ~5.2 ka. However, a lack of lowland vegetation records has prevented a detailed evaluation of forest response to Holocene climate change. Additionally, although modern vegetation communities are linked to human disturbance, few studies have addressed how prehistoric human activities helped engineer the character of modern African ecosystems. Understanding the architecture of lowland and highland forests is important to prevent further degradation from climate/land-use change. We present an 11,000 yr fossil pollen record from Lake Edward, Uganda. We show that Guineo-Congolian forests dominated the highlands and lowlands in equatorial East Africa in the early Holocene, highlighting the importance of rainfall and temperature in controlling forest communities. These forests remained until ~5.2 ka, when the climate became drier. The lacustrine ecosystem response to aridification was abrupt; however, forest decreased gradually, replaced by deciduous woodlands. Woodlands dominated until after an arid period at 2 ka; however, forest did not recover. Increased disturbance indicators and grasses suggest that the arrival of Iron Age people resulted in the modern fire-tolerant vegetation. Although late Holocene climate played a role in vegetation opening, the modern ecosystem architecture in East Africa is linked to early human activities.