AbstractAimsTrends in the extent of habitat types and species frequencies might not follow a simple pattern. However, data that are able to link those trends are scarce. Here, we use data from a repeated habitat mapping program to test consistency between habitat type and species change.LocationFederal state of Baden‐Württemberg, Germany.MethodsWe derived temporal trends over several decades concerning: (a) the extent of all protected habitat types across the state, (b) plant species across the state, and (c) plant species within habitat types. We tested the consistency between trends in the extent of every protected habitat type with trends of those species that prefer that particular habitat type, as well as with mean trends of all species that occur within that particular habitat type.ResultsWe found that, on average, most protected habitat types decreased in area, with the exception of forests, which showed positive trends. Species analysis showed positive trends for species preferring the habitat types scrubs, copses and field hedges, as well as bog, carr, swamp and alluvial forests. By contrast, negative trends were found for species preferring the habitat types heaths and semi‐natural grasslands, meadows and pastures. While non‐native species increased, species that were considered endangered decreased. A species’ trend across Baden‐Württemberg mostly followed the trend of the species’ preferred habitat type. However, within some habitat types, the mean species’ trend did not follow the trend of those habitat types’ extent. Decreasing species within habitat types were especially those that preferred each particular habitat type.ConclusionsOur results point to an ongoing turnover of floristic composition, and thus to changes in habitat quality within habitat types. This implies that future monitoring programs should track temporal trends of both habitat types and the species occurring in these habitat types as a measure of habitat quality, because they can show diverging trends.