Natura 2000 is a European network of sites dedicated to the conservation of vulnerable habitats. The definitions of Natura 2000 habitats are mainly based on plant communities. We investigated if the increase of the dominance of warm-adapted species observed in plant communities, described as thermophilization, had already led to measurable changes in Natura 2000 forest habitats. We created 5701 pairs of neighboring forest plots by gathering plots surveyed before 1987 and after 1997 to reflect historical and recent climatic conditions. A Natura 2000 habitat type was assigned to each vegetation plot using an automatic classification program. We calculated a temperature index that synthesized the temperature range of each habitat, and compared the habitat temperature indexes of the recent and historical plots of each pair. We highlighted a significant overall shift of 4.8% ± 1.78 (CI 95%) of the pairs toward warmer habitats over the studied period. While the shift was not significant in lowlands, 11.1% ± 3.0 (CI 95%) of the pairs evolved toward warmer habitats in highlands. The excess of pairs with a warmer habitat in the recent period was interpreted as thermophilization of Natura 2000 forest habitats. Therefore, global warming has been strong enough to induce actual changes at the coarse-grained habitat resolution specifically targeted by public policies. The absence of significant results in lowlands suggests the existence of unrealized potential habitat changes, which can be considered as a climatic debt. These results call for differential prioritization levels and implementations of public policies for nature conservation in lowlands and highlands.