AbstractDetecting species trends across different habitat types and larger regions is required to generate a general and reliable foundation for conservation planning. While direct monitoring data covering a large spatial and temporal extent are mostly lacking, data collected for other purposes than monitoring can be considered to detect trends. Here we analyzed both habitat type and plant species trends over several decades (1979–2017), using repeated habitat survey data from the habitat mapping program of the city and federal state of Hamburg. Next to transitions between habitat types, we looked for differences between winner and loser species, considering also their habitat type preference, red list, and non‐native status. Furthermore, we assessed the consistency between trends of habitat types and species that are characteristic of those habitat types. We found declines in habitat area of semi‐natural (semi‐)dry grasslands and semi‐ruderal vegetation and increases in habitat area of species‐poor grasslands, pioneer forests, and human settlements. More species showed positive than negative trends over time, with winners including many forest and scrub as well as non‐native species, while losers were represented mostly by endangered and ruderal species. Most habitat types included a mixture of both winner and loser species. Habitat type trends were mostly not reflected in trends of species that were characteristic of a particular habitat, such as semi‐natural (semi‐)dry grasslands. This can be explained, on the one hand, by species extinction debts, and on the other hand, by a low habitat specificity of some species that find refuges also in secondary habitats. Our study not only shows the difficulties but also offers methods on how to use repeated habitat mapping data to detect trends for habitat types and plant species. In contrast to monitoring programs focusing on individual endangered habitats, results from repeated habitat surveys allow the identification of those secondary habitats of a species that might contribute the most to preserving populations of their primary habitat.