We test the hypothesis that climatic changes since 1800 have resulted in unrealized potential vegetation changes that represent a “climatic debt” for many ecosystems. Caledonian pinewoods, an EU priority forest type, are used as a model system to explore potential impacts of two centuries of climatic change upon sites of conservation importance and surrounding landscapes. Using methods that estimate topographic microclimate, current and preindustrial climates were estimated for 50 m grid cells and simulations made using a dynamic vegetation model. Core Caledonian pinewood areas are now less suitable for growth of pine and more favorable for oak than in 1800, whereas landscapes as a whole are on average more favorable for both. The most favorable areas for pine are now mainly outside areas designated to conserve historical pinewoods. A paradigm shift is needed in formulating conservation strategies to avoid catastrophic losses of this habitat, and of many others globally with trees or other long-lived perennials as keystone species.