The positive effect of fully protected Marine Protected Areas (MPAs) on marine biodiversity, specifically on fishes, has been widely documented. In contrast, the potential of MPAs to mitigate the impact of adverse climatic conditions has seldom been investigated. Here, we assessed the effectiveness of MPAs, quantified as increasing fish biomass, across wide geographic and environmental gradients across the Mediterranean Sea. We performed underwater visual surveys within and outside MPAs to characterize fish assemblages in 52 rocky reef sites across an extent of over 3,300 km. We used the steep spatial temperature gradient across the Mediterranean as a ‘space-for-time’ substitution to infer climate-driven temporal changes. We found that, as expected, Mediterranean MPAs increased fish biomass. At the same time, higher seawater temperatures are associated with decreased fish biomass, changes in species composition, and shifts towards more thermophilic species. Importantly, we found that the rate of decrease in fish biomass with temperature was similar between protected and fished sites. Taken together, these results suggest that the capacity of MPAs to harbor higher fish biomass, compared to surrounding areas, is maintained across a broad temperature range. At the same time, MPAs will not be able to offset larger-scale biotic alterations associated with climate change. Policy implications: Our results suggest that sustained warming will likely reduce fish biomass in the Mediterranean Sea and shift community structure, requiring more conservative targets for fishery regulations. At the same time, protection from fishing will remain an important management tool even with future high-water temperatures, and MPAs are expected to continue to provide local-scale benefits to conservation and fisheries.