Abstract Assessing temporal changes in plant communities is a core aim of temporal ecology and a shared priority of global conservation agendas which is particularly urgent in threatened ecosystems. Mediterranean coastal dunes harbour some of the most threatened habitats in Europe. Yet, surprisingly, studies capturing the recent temporal dynamics of biodiversity in these systems by accounting for multiple diversity facets and different aspects of community structure are missing. Here, using data from a resurveying study, we provide a first comprehensive, habitat‐based, multi‐faceted assessment of recent (10–15 years) temporal changes in threatened Mediterranean coastal dunes. To this aim, we quantified taxonomic and functional changes in plant communities using indices capturing multiple biodiversity features, and we explored trends at both the community level and the species level. We compared observed biodiversity changes across habitats (to look for evidence of generalized biodiversity loss) and across facets (to infer the potential loss of unique functions), and tested their significance using a null model. Overall, we predicted large compositional shifts and biodiversity loss beyond expectations in many communities, although with differences among habitat types. Our results reveal severe shifts in the taxonomic profile of the communities, mostly driven by a non‐random species loss, and little temporal overlap in functional space, implying large changes in both community structure and ecological strategies of the investigated habitats. This, together with the disappearance of c. 23% of historical plots and with substantial losses in focal species, suggests that intense degradation processes are occurring in coastal dune habitats, particularly on the upper beach and on shifting dunes. Synthesis. This study provides the first evidence of large, often non‐random, taxonomic and functional changes occurring in Mediterranean coastal dune plant communities in a surprisingly short time‐span. Along with furthering our knowledge of the recent dynamics affecting these endangered ecosystems, our results also pinpoint the types of habitats that are most at risk, helping to direct future conservation efforts and management. Future research should now be directed at more precisely testing potential drivers of these changes.