We used 474 European plant species to analyse the impacts of climate and land-use change on the composition of habitat-specific species pools in Germany. We quantified changes in the probability of occurrence of species in a grid cell using an ensemble of three statistical modelling techniques, namely generalized linear models (GLMs), generalized additive models (GAMs) and random forests (RFs), under three scenarios (average change +2.2, +2.9, and +3.8°C up to 2080). We evaluated the impact on single species occurrence and resulting species pools considering their affiliation to ten major terrestrial habitat types in both current (1961-90) and future projections (2051-80). Current habitat-specific species pools declined in size across all scenarios, e.g. by 24 ± 13% (mean ± s.d.) under the most severe scenario. We show that species responses may strongly vary among scenarios and different habitats with a minimum average projected range loss of 14% (±18%; species typical to urban habitats under moderate climate change assumptions, average temperature increase +2.2°C) to a maximum average projected range loss of 56% (±29%; species assemblages from mountain communities below the alpine zone at +3.8°C). A separate analysis of species composition in habitat-specific species pools revealed a significant interaction between the scenario and the major habitat classes. We found a higher risk for habitat types with high conservation value characterised by a significant association between number of nationally endangered species and projected range loss in major habitats. Thus, habitat-specific management and application of measures favouring dispersal are required for mitigation of climate change impacts.