Protected areas are central to biodiversity conservation. For marine fish, marine protected areas (MPAs) often harbour more individuals, especially of species targeted by fisheries. But precise pathways of biodiversity change remain unclear. For example, how local-scale responses combine to affect regional biodiversity, important for managing spatial networks of MPAs, is not well known. Protection potentially influences three components of fish assemblages that determine how species accumulate with sampling effort and spatial scale: the total number of individuals, the relative abundance of species and within-species aggregation. Here, we examined the contributions of each component to species richness changes inside MPAs as a function of spatial scale. Using standardized underwater visual survey data, we measured the abundance and species richness of reef fishes in 43 protected and 41 fished sites in the Mediterranean Sea. At both local and regional scales, increased species evenness caused by added common species in MPAs compared to fished sites was the most important proximate driver of higher diversity. Site-to-site variation in the composition (i.e. β-diversity) of common species was also higher among protected sites, and depended on sensitivity to exploitation. There were more abundant exploited species at regional scales than at local scales, reflecting a tendency for different protected sites to harbour different exploited species. In contrast, fewer abundant unexploited species were found at the regional scale than at the local scale, meaning that relative abundances at the regional scale were less even than at the local scale. Synthesis and applications. Although marine protected areas (MPAs) are known to strongly influence fish community abundance and biomass, we found that changes to the relative abundance of species (i.e. increased evenness) dominated the biodiversity response to protection. MPAs had more relatively common species, which in turn led to higher diversity for a given sampling effort. Moreover, higher β-diversity of common species meant that local-scale responses were magnified at the regional scale due to site-to-site variation inside protected areas for exploited species. Regional conservation efforts can be strengthened by examining how multiple components of biodiversity respond to protection across spatial scales.