The tropical alpine ecosystem in eastern Africa is highly fragmented among biological ‘sky islands’, where populations of frost-tolerant organisms are isolated from each other by a ‘sea’ of tropical lowlands. One-third of the species in the afroalpine flora are exclusively alpine, but the other species can to varying degrees extend into grasslands and open forests of lower vegetation belts. A long-debated question is whether colonization of the alpine zone of these mountains and subsequent intermountain gene flow entirely depend on long-distance dispersal across unsuitable habitats, or whether suitable habitats shifted far enough downslope under past colder climates to form bridges enabling gradual migration. Here we address this question using a classification tree model. We mapped the extent of the current alpine habitat and projected it to the last glacial maximum (LGM) climate to assess whether gradual migration was possible for exclusively alpine taxa during this glacial period, and thus potentially also during earlier Pleistocene glaciations. Next, we modelled landcover under current and LGM climates to assess whether grassland and open forests could have served as migration corridors for alpine taxa that today extend into lower vegetation belts. We estimated that the LGM treeline was about 1000 m lower and the alpine habitat was about eight times larger than that today. At the LGM, we found that most of the currently fragmented alpine habitat of the Ethiopian highlands was interconnected except across the Great Rift Valley, whereas the solitary mountains of East/Central Africa remained isolated for exclusively alpine species. However, for drought-tolerant alpine species that today extend below the treeline, gradual migration through habitat corridors may have been possible among mountains during the dry glacial periods, and possibly also under the current climate before agriculture transformed the low-lying landscapes.