The need and will to mitigate and adapt to climate change and its threats to biodiversity have risen. Nevertheless, the acting for the conservation of biodiversity remains hampered by knowledge gaps. E.g., for habitat types (in the sense of biotopes) the impact of climate change has been scarcely researched. There are many “species distribution models” (SDMs) that can project species distributions under climate change, but their application to contemporary habitat types poses considerable methodological problems. Here we show the viability of the uncommon method of “climate analogues” to provide data to assess the potential impact of future climate change on habitat types for chosen regions, and the usability of the method compared to SDMs.We assume climate analogues can reflect the potential future habitat data in the study regions when (1) plausibly located future climate analogues are found with relevant climate variables for the studied habitat types, and (2) habitat occurrences relate with their frequency and area to the climate reflected in the climate analogues. We tested the method for three landscapes in Germany using European Natura 2000 habitat data, analyzing five future climate conditions until 2100. Future climate analogues were found southwest of the study regions, primarily in France. They progressed further southwest and from higher to lower elevations with increasing climate change. Ecologically sound habitat types remained stable, increased, and decreased in frequency and area parallel to the magnitude of climate change in the climate analogues. Thus, we regard climate analogues as a viable method to estimate potential climate change induced changes of Natura 2000 habitat types at the regional scale. Nature conservation benefits from climate analogues as they are efficient, data-robust, and promote the implementation of actions, the exchange of conservation experiences, and international collaboration. They are an easy and powerful method to tackle the looming losses of habitat diversity from climate change.