Aim  Species distribution models have been used frequently to assess the effects of climate change on mountain biodiversity. However, the value and accuracy of these assessments have been hampered by the use of low-resolution data for species distributions and climatic conditions. Herein we assess potential changes in the distribution and community composition of tree species in two mountainous regions of Spain under specific scenarios of climate change using data with a high spatial resolution. We also describe potential changes in species distributions and tree communities along the entire elevational gradient. Location  Two mountain ranges in southern Europe: the Central Mountain Range (central west of the Iberian Peninsula), and the Iberian Mountain Range (central east). Methods  We modelled current and future distributions of 15 tree species (Eurosiberian, sub-Mediterranean and Mediterranean species) as functions of climate, lithology and availability of soil water using generalized linear models (logistic regression) and machine learning models (gradient boosting). Using multivariate ordination of a matrix of presence/absence of tree species obtained under two Intergovernmental Panel on Climate Change (IPCC) scenarios (A2 and B2) for two different periods in the future (2041–70 and 2071–2100), we assessed the predicted changes in the composition of tree communities. Results  The models predicted an upward migration of communities of Mediterranean trees to higher elevations and an associated decline in communities of temperate or cold-adapted trees during the 21st century. It was predicted that 80–99% of the area that shows a climate suitable for cold–wet-optimum Eurosiberian coniferous and broad-leaved species will be lost. The largest overall changes were predicted for Mediterranean species found currently at low elevations, such as Pinus halepensis, Pinus pinaster, Quercus ilex ssp. ballota and Juniperus oxycedrus, with sharp increases in their range of 350%. Main conclusions  It is likely that areas with climatic conditions suitable for cold-adapted species will decrease significantly under climate warming. Large changes in species ranges and forest communities might occur, not only at high elevations within Mediterranean mountains but also along the entire elevational gradient throughout this region, particularly at low and mid-elevations. Mediterranean mountains might lose their key role as refugia for cold-adapted species and thus an important part of their genetic heritage.