Accurate estimates of historical forest extent and associated deforestation rates are crucial for quantifying tropical carbon cycles and formulating conservation policy. In Africa, data-driven estimates of historical closed-canopy forest extent and deforestation at the continental scale are lacking, and existing modelled estimates diverge substantially. Here, we synthesize available palaeo-proxies and historical maps to reconstruct forest extent in tropical Africa around 1900, when European colonization accelerated markedly, and compare these historical estimates with modern forest extent to estimate deforestation. We find that forests were less extensive in 1900 than bioclimatic models predict. Resultantly, across tropical Africa, ~ 21.7% of forests have been deforested, yielding substantially slower deforestation than previous estimates (35–55%). However, deforestation was heterogeneous: West and East African forests have undergone almost complete decline (~ 83.3 and 93.0%, respectively), while Central African forests have expanded at the expense of savannahs (~ 1.4% net forest expansion, with ~ 135,270 km2 of savannahs encroached). These results suggest that climate alone does not determine savannah and forest distributions and that many savannahs hitherto considered to be degraded forests are instead relatively old. These data-driven reconstructions of historical biome distributions will inform tropical carbon cycle estimates, carbon mitigation initiatives and conservation planning in both forest and savannah systems.