Protected areas are generally designed to conserve biodiversity. However, how well they also contribute to maintaining ecosystem functions that plant diversity supports has rarely been explicitly tested, often due to the lack of historical ecosystem function data. Here, we used a trait-based approach to reconstruct past ecosystem functioning and examine changes in functions over the last 15 years in protected and unprotected coastal dune ecosystems, checking where functions remain stable over time. First, we resurveyed vegetation in quasi-permanent plots and measured in the present several ecosystem functions related to productivity, carbon, water, nutrient cycling, erosion control, and invasion resistance across six coastal dune sites in Central Italy. Second, using these data, we quantified Biodiversity-Ecosystem Function (BEF) relationships and employed them to hindcast past ecosystem functions based on historical vegetation surveys. Finally, as a case study, we applied this method to assess temporal changes in ecosystem functioning under three protection regimes: national protected areas (i.e. strict protection), Natura 2000 sites (loose protection), and non-protected areas. Productivity, carbon, and water regulation increased over time in non-protected areas, likely due to an expansion of ruderal and non-native species, that are usually more productive. Within Natura 2000 sites, communities showed a decrease in erosion control and invasion resistance potential, due to the loss of important dune-building species and the spread of non-natives. Only within national protected areas, ecosystem functions did not undergo significant temporal changes, and invasion resistance even increased. Our results suggest that in the study area ecosystem functioning remain stable over time only in areas under strict protection. More broadly, our study demonstrates the potential for using revisitation data in combination with locally estimated BEF relationships to hindcast past ecosystem functioning, providing a valuable tool for monitoring long-term functional changes in response to conservation measures.