Marine Protected Areas (MPAs) have been proved to effectively protect and restore fish assemblages. There is mixed evidence regarding the effects of MPAs on benthic assemblages, habitat complexity, and how protection might mediate the effects of habitat features (including biotic and abiotic components) on fish assemblages, with very little information concerning temperate areas. Here, our aim is to assess how protection 1) influences benthic assemblages and habitat complexity, and 2) mediates the effects of habitat complexity on fishes.Using non-destructive methods (photosampling for shallow rocky benthic assemblages, and underwater visual census using strip transects for fish assemblages) to characterize benthic and fish assemblages, we sampled 15 Mediterranean locations, each including protected and unprotected sites. In all, we sampled 90 sites, and analyzed 2,760 photos and 800 replicated transects, gathering information on 44 benthic and 72 fish taxa. Abiotic, biotic and synthetic (i.e. combining the previous two) complexity indices have been computed to synthesize habitat features. Overall, whole benthic assemblages did not significantly differ between protected and unprotected conditions, but higher cover of the ecologically important erect algae belonging to the genus Cystoseira sensu lato was recorded within MPAs. Abiotic, biotic and synthetic complexity did not show clear patterns related to protection levels, displaying inconsistent responses between different locations. Our findings highlight that protection has a generally positive effect on fish biomass, this latter variable responding independently of the habitat complexity.Our study, in conclusion, confirms that MPAs can be effective to protect and restore rocky-reef assemblages, highlighting the need for more in-depth exploration of the mechanisms determining the different responses of benthic taxa to protection and how this can influence the associated fish assemblages.