Aims The effect of biogeographical processes on the spatial turnover component of beta‐diversity over large spatial extents remains scarcely understood. Here, we aim at disentangling the roles of environmental and historical factors on plant taxonomic and phylogenetic turnover, while controlling for the effects of species richness and rarity. Location European beech (Fagus sylvatica) forests in Europe. Methods We aggregated plant species occurrences from vegetation plots in spatial grid cells of 0.25º × 0.25º to calculate the spatial turnover component of taxonomic (TBDturn) and phylogenetic (PBDturn) beta‐diversity for each cell. We also calculated the deviation of PBDturn given TBDturn (PBDdev‐turn), which measures the importance of phylogenetic turnover after factoring out taxonomic turnover. Beta‐diversity was calculated for each grid cell as the mean pairwise dissimilarity between the focal cell and all other cells. We used structural equation modeling (SEM) to examine the relationships between environmental (climate, soil pH, and distance from the geographical distribution limit of beech) and historical (distance from beech glacial refugia) predictors and beta‐diversity metrics. Results We found a geographically consistent variation in taxonomic and phylogenetic turnover. Overall, TBDturn and PBDturn increased significantly toward more extreme climatic conditions, on more acidic soils, and toward the margins of beech distribution. The effects of environmental variables and the distance from glacial refugia on beta‐diversity metrics were mediated by species richness and rarity. Phylogenetic turnover was low in relation to taxonomic turnover (i.e., high PBDdev‐turn) in areas closer to glacial refugia. Conclusions Continental‐scale patterns of beta‐diversity in European beech forests are the result of complementary ecological and evolutionary processes. In general, beech forests are taxonomically and phylogenetically more distinct in climatically marginal areas of their European range. However, the spatial variation of beta‐diversity in European beech forest flora is still strongly characterized by the distribution of groups of closely related species that evolved or survived in glacial refugia. We examined the relative roles of environmental and historical factors in driving taxonomic and phylogenetic turnover of European beech (Fagus sylvatica) forests. We showed that beech forests are more compositionally distinct in climatically marginal areas of their range, and that the spatial variation of beta‐diversity is strongly influenced by the distribution of groups of closely related species in glacial refugia.