New deforestation and selective logging data and climate change projections suggest that biodiversity refugia in humid tropical forests may change more extensively than previously reported. However, the relative impacts of climate change and land use vary by region. In the Amazon, a combination of climate change and land use renders up to 81% of the region susceptible to rapid vegetation change. In the Congo, logging and climate change could negatively affect the biodiversity in 35–74% of the basin. Climate-driven changes may play a smaller role in Asia-Oceania compared to that of Latin America or Africa, but land use renders 60–77% of Asia-Oceania susceptible to major biodiversity changes. By 2100, only 18–45% of the biome will remain intact. The results provide new input on the geography of projected climate change relative to the ongoing land-use change to better determine where biological conservation might be most effective in this century.