Abstract The European Habitat Directive encompasses a conservation policy devoted to conserve habitats rather than single species. This ambition has strong ecological justifications, and inspires other initiatives such as the IUCN red list of ecosystems. Evaluating this policy is therefore pivotal to identify and reproduce best practices. However, the habitat aspect of this policy has so far not been systematically assessed. To make up for this lacuna, we take advantage of decision‐aiding methodologies to introduce a new normative framework. According to this framework, a conservation policy is positively evaluated if it contributes to conservation, is science‐based, operational, and legitimate. Based on an exploration of the published literature and unpublished reports and databases, we identify knowledge gaps plaguing the European habitat conservation policy. We argue that, due to these knowledge gaps, the contribution of this policy to the conservation of habitats is unproven, it is not science‐based, not operational and not legitimate. Our study draws heavily on the French implementation. Analyzing this example, we highlight knowledge gaps that carry lessons for European conservation policies as a whole, but also for conservation initiatives focused on habitats in a broader geographical and political context. We then identify concrete means to strengthen habitats conservation policies.