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Aim Climate is an important factor controlling plant distributions. However, it is not yet fully understood how climate interacts with human impacts or whether the effects of these factors differ between native and alien species. Facing ongoing climate change and urbanization, we explore the effects of climate on plant species richness and composition across European cities. Location Sixty cities in Western, Central and Southern Europe. Taxon Vascular plants. Methods Species presence was recorded in seven habitats in each city. Large-scale climatic gradients were derived from 22 climatic variables using a partial principal component analysis that controlled for the effects of human population size and gross domestic product. The effects of climate and habitat type on the numbers of native and alien species were tested using linear mixed-effect models. The native and alien compositional variation across cities and habitats was analysed using principal component analysis with variation partitioning. Results The Mediterranean-to-temperate climatic gradient had a significant effect on species numbers across all habitats. The numbers of both native and alien species increased from the Mediterranean to temperate Europe. Within each city, the proportion of alien species decreased from highly urbanized to less urbanized habitats. Climate had a stronger effect on the composition of alien plants than on the composition of native plants. The native species composition especially changed from the Mediterranean to temperate cities and alien species composition also from oceanic to continental cities. Main conclusions Urban native and alien species richness follow the pattern found for the whole European flora. Based on this observation, we suggest that the future shift of warm and dry conditions from the Mediterranean to the north that is expected under global change scenarios could affect richness and change the composition of European urban floras. However, this shift would not necessarily alter the proportions of aliens.