Questions Semi‐natural habitats are threatened by shifts in management with worrying effects on multiple facets of biodiversity. We revisited sites once representing a reference for a calcareous semi‐natural grassland habitat aiming to: (a) identify the drivers of taxonomic, functional and phylogenetic diversity, and habitat conservation state; (b) assess the role of characteristic and derived diversity in determining these patterns; and (c) discuss the possibility of reconciling the goals of habitat conservation and enhancement of different facets of plant diversity. Location Seven sites along the Apennines (Italy), from Mt. Catria (43.46206° N, 12.70397° E) to Mt. Alpi (40.11768° N, 15.98341° E). Methods For 132 revisited plots, we calculated vascular plant taxonomic, functional and phylogenetic diversity using Hill numbers, and used boosted regression trees to investigate their response to the compositional dissimilarity from historical plots, to grazing intensity and to environmental variables. We identified characteristic and derived diversity and summarized them in an index of habitat conservation state whose drivers were investigated using the same approach. Results Plant diversity was influenced by the site, whereas the habitat conservation state responded more markedly to vegetation type. Grazing intensity, slope and soil variables drove taxonomic and functional diversity, and the habitat conservation state, with some differences in their relative importance. Phylogenetic diversity responded only partly to grazing intensity, while it showed a major response to increasing temperatures. Conclusions Patterns and drivers of different facets of plant diversity partially differ from those of the habitat conservation state, suggesting that the management of semi‐natural habitats should be carefully tailored on specific conservation objectives. Generalized actions on grazing regimes and litter removal can promote habitat conservation, whereas the outcomes of these actions for plant diversity may differ across sites. Identifying areas particularly subjected to land‐use changes and/or climate warming may drive conservation actions. By revisiting reference sites of calcareous semi‐natural grasslands, we found different patterns and drivers of plant diversity and habitat conservation state. Vegetation deviation from the habitat reference state, taxonomic and functional diversity mainly respond to grazing regimes, while phylogenetic diversity does to climate warming.