The overexploitation of many marine resources and ecosystems calls for the development and implementation of measures to support their recovery and conservation. The potential contributions to support fisheries and ecosystem recovery were assessed at the local level of the three multiple-use marine protected areas (MPAs) of Cerbère-Banyuls, Medes Islands, and Cap de Creus, located in the north-western Mediterranean Sea. For each MPA, a food-web model accounting for each protection level (PL) was developed: the fully protected area (FPA), the partially protected area (PPA) and the unprotected area (UPA) surrounding the MPA. Using the resulting nine food-web models, the ecosystem structure and functioning of each PL were compared and characterized, differences and similarities within and among the three MPAs were assessed, and ecosystem response to full protection was evaluated for the three MPAs. Differences in terms of ecosystem structure and functioning were found among PLs. Overall, FPAs presented the most positive effect of protection in terms of ecosystem structure and functioning, followed by PPAs. However, the effects of protection on neighbouring UPAs were hardly noticeable. Similarities between Cerbère-Banyuls and Medes Islands MPAs were observed, while Cap de Creus MPA showed the least benefits from protection overall. These results are likely to be due to similarities in the configuration of the protected areas, the levels of enforcement and compliance, and the impact of recreational and small-scale fisheries allowed in the PPAs and UPAs. This study illustrates that well-enforced Mediterranean MPAs, even when small, can yield local positive impacts on the structure and functioning of marine ecosystems that can contribute to support local fisheries.