With the rapid global increase in the number and extent of marine protected areas (MPAs), there is a need for methods that enable an assessment of their actual contribution to biodiversity conservation. In Brazil, where MPAs have been designated to replenish biodiversity, there is a lack of regional-scale analysis of MPA impacts and the factors related to positive ecological change. This study aims to quantify the magnitude of the ecological effects of Brazilian MPAs and test whether some study and MPA characteristics (e.g., taxonomic group studied, exploitation level of species, MPA area, protection time, management effectiveness, level of connectedness, etc.) were underlying factors associated with their performance. We conducted a structured search in a database of scientific articles, selecting comparative studies of direct biodiversity metrics inside and outside MPAs offering different protection levels (i.e., fully- or partially-protected MPAs) or within MPAs with distinct zones. We then carried out a meta-analysis based on 424 observations found in 18 articles. Averaged across all studies, we found that MPAs had a 17% increase in the abundance of species, length of individuals, and community diversity. When compared to open-access areas, fully-protected MPAs increased biodiversity by 45%. However, MPAs offering partial protection had variable effects, ranging from significant positive to significant negative effects. MPA effects depended on the taxonomic group and exploitation level of species, with the strongest positive effects seen on exploited fish species and benthic invertebrates. Partially-protected MPAs that reported strong positive effects required long time of protection (>15years) and high level of connectivity. Conversely, fully-protected MPAs (i.e., no-take ones) could be effective even when small, under intense fishing pressure in their surroundings, and regardless of their level of connectivity. We used the Brazilian MPAs as a case study, but these results can contribute to a more comprehensive assessment of the association between ecological impacts of MPAs and drivers of conservation success, and offer key information to consolidate MPA networks that sustain biodiversity.