Though protected areas are recognized as the cornerstone of global conservation efforts, their effectiveness in safeguarding biodiversity is currently debated. In particular, studies evaluating the counterfactual influence of protection status on community metrics derived from field-collected data are still scarce. In this paper, using data from a resurveying study, we assessed the contribution of the European Natura 2000 network to maintaining and/or improving through time habitat quality and functional integrity in Mediterranean coastal dune habitats, which appear among the most threatened ecosystems worldwide. Using multiple regression techniques, we tested the influence of protection status on habitat loss and on 10-15 years changes in the richness and cover of two highly informative plant groups: focal and alien species. Next to a substantial habitat loss, we observed an overall decrease in focal species richness and cover, whereas alien species were stable or slightly increasing, depending on the habitat. Surprisingly, changes in the analyzed metrics did not differ between protected and non-protected sites, thus providing no substantial evidence of the effectiveness of Natura 2000 in conserving and/or improving dune habitats. Taken together, such results suggest negative implications for the whole ecosystem structure and functionality, to be expected regardless of the protection status. This led us to reflect about the general inadequacy in the implementation of actual conservation measures in coastal habitats, discuss potential causes (lack of ad-hoc management plans and targeted conservation measures, scarcity of dedicated funding, bureaucratization), and stress the value of monitoring activities for evaluating conservation outcomes and reformulating current strategies.