Marine protected areas (MPAs) can be a useful tool to manage coastal ecosystems, delivering both social and ecological outcomes. However, in many instances, relevant data is missing to conduct proper impact assessments, which is key to identifying ecological and social synergies and potential trade‐offs, and to adapting management according to local objectives. The ecological effects of an MPA established in Palawan, Philippines, in 2016, were assessed. The most common species targeted by fisheries were identified by local fishers. Species size and number were collected through underwater visual census with n = 288 belt transects assigned in different sites and locations to ensure to provide both protected and control (fished) sites for the MPA assessment, and baseline data for three new MPAs that were created in 2022. 91 coral‐reef fish species belonging to 12 families were recorded. Mixed effect linear regression was used to compare target fish populations in protected and control sites. Compared to control locations, 5 years after its implementation, the MPA showed significantly higher species richness, abundance, mean size, and biomass while no significant difference was found on the average trophic level between MPA and control sites. Monitoring the early effects of an MPA and collecting baseline data prior the implementation of an MPA network is key for adaptive management.