Marine protected areas (MPAs) are a cornerstone of marine conservation. Globally, the number and coverage of MPAs are increasing, but MPA implementation lags in many human-dominated regions. In areas with intense competition for space and resources, evaluation of the effects of MPAs is crucial to inform decisions. In the human-dominated Mediterranean Sea, fully protected areas occupy only 0.04% of its surface. We evaluated the impacts of full and partial protection on biomass and density of fish assemblages, some commercially important fishes, and sea urchins in 24 Mediterranean MPAs. We explored the relationships between the level of protection and MPA size, age, and enforcement. Results revealed significant positive effects of protection for fisheries target species and negative effects for urchins as their predators benefited from protection. Full protection provided stronger effects than partial protection. Benefits of full protection for fish biomass were only correlated with the level of MPA enforcement; fish density was higher in older, better enforced, and -interestingly- smaller MPAs. Our finding that even small, well-enforced, fully protected areas can have significant ecological effects is encouraging for "crowded" marine environments. However, more data are needed to evaluate sufficient MPA sizes for protecting populations of species with varying mobility levels.