During the late Quaternary, extensive forests covered the slopes of the southern section of the Lebanon Mountains. Investigating the response of these forests to the climate change at the Last Interglacial—Last Glacial transition provides insight into their response to an abrupt and extensive deterioration in climate. Here we present the results of a new sedimentary sequence from the southern Bekaa Valley, Lebanon, which spans the late Last Interglacial marine isotope stage (MIS) 5e to early MIS 5c of the Last Glacial. High-resolution analyses for pollen, carbon isotopes and total organic carbon have been undertaken and reveal dramatic shifts in the vegetation composition during this transition. At the Last Interglacial (MIS 5e) to glacial (MIS 5d) transition an environmental threshold was crossed in response to a significant reduction in precipitation with the development of grassland/steppe dominated by Chenopodiaceae and Artemisia. The arid conditions led to the loss of the temperate deciduous arboreal species (Betula, Alnus and Corylus) and significant reduction in the populations of coniferous trees Cedrus libani and Pinus that populated the slopes of the Lebanon Mountains during the Last Interglacial. At the onset of the MIS 5c interstadial an increase in arboreal pollen is observed, in particular Cedrus libani, as the grassland/steppe transitioned into an open forest-steppe. The response of the vegetation during the Last Interglacial to temperatures that were at least as high as or higher than present, and the onset of the Last Glacial, when precipitation declined significantly, has the potential to indicate how eastern Mediterranean biotic communities will respond to changes in these climatic parameters that are predicted to occur in the near future.