The success of MPAs in conserving fishing resources and protecting marine biodiversity relies strongly on how well they meet their planned (or implicit) management goals. From a review of empirical studies aiming at assessing the ecological effects of Mediterranean and Macaronesian MPAs, we conclude that establishing an MPA is successful for (i) increasing the abundance/biomass, (ii) increasing the proportion of larger/older individuals, and (iii) enhancing the fecundity of commercially harvested populations; also, MPAs demonstrated to be effective for(iv)augmenting local fishery yields through biomass exportation from the protected area, and(v) inducing shifts in fish assemblage structure by increasing the dominance of large predator species. However, the attraction for tourism and diving due to ecological benefits of protection can cause damages likely to reverse some of the MPA effects. Other expected effects are more subject to uncertainty, and hence need more research, such as(vi) causing density-dependent changes in life history traits and (vii) protecting the recruitment of commercially important species, (viii) protecting marine biodiversity (including genetic diversity),(ix) causing ecosystem-wide effects such as trophic cascades, and (x) increasing community and ecosystem stability, thus promoting resilience and faster recovery from disturbance. Meta-analysis of data arising from these case studies are used to establish the overall effect of MPAs, and its relationship to MPA features, such as size of no-take area or time since protection. Based on the review and the meta-analyses, specific recommendations are provided for MPA management, regarding the establishment of goals and objectives, site selection, MPA design and zoning, planning, and monitoring. Finally, a series of recommendations for MPA research are offered to drive future research in MPA issues in the Mediterranean and Macaronesia.