Island biogeographical models consider islands either as geologically static with biodiversity resulting from ecologically neutral immigration–extinction dynamics1, or as geologically dynamic with biodiversity resulting from immigration–speciation–extinction dynamics influenced by changes in island characteristics over millions of years2. Present climate and spatial arrangement of islands, however, are rather exceptional compared to most of the Late Quaternary, which is characterized by recurrent cooler and drier glacial periods. These climatic oscillations over short geological timescales strongly affected sea levels3, 4 and caused massive changes in island area, isolation and connectivity5, orders of magnitude faster than the geological processes of island formation, subsidence and erosion considered in island theory2, 6. Consequences of these oscillations for present biodiversity remain unassessed5, 7. Here we analyse the effects of present and Last Glacial Maximum (LGM) island area, isolation, elevation and climate on key components of angiosperm diversity on islands worldwide. We find that post-LGM changes in island characteristics, especially in area, have left a strong imprint on present diversity of endemic species. Specifically, the number and proportion of endemic species today is significantly higher on islands that were larger during the LGM. Native species richness, in turn, is mostly determined by present island characteristics. We conclude that an appreciation of Late Quaternary environmental change is essential to understand patterns of island endemism and its underlying evolutionary dynamics.