While marine protected areas (MPAs) are increasing worldwide, it is still needed to assess the effectiveness of those already consolidated. Methods and ecological assessments to understanding integrated and habitat-specific management regimes are still scarce and insufficient for policy implications and biodiversity conservation. Through Baited Remote Underwater Video (BRUV), we used fish assemblages as proxy of ecological and managerial status in two reef habitat types along three protection levels at Abrolhos Bank - the largest and most biodiverse coral reef complex of the South Atlantic. We found completely distinct responses in the fish fauna between the top (shallow) and bottom (deep) habitats of the unique "chapeirões" pinnacle reef formations. In the most protected zone (no-take), higher richness and abundance of commercial fish and more diverse trophic structure was observed. Particularly, large (sharks and groupers) and small carnivores (snappers) were more abundant and distributed more homogeneously over both reef habitats in the strictly enforced no-take zone. Abundance of these top-predators decreased from the low enforcement no-take zone to the multiple use area, where they were often absent while their typical preys (primary and secondary consumers) were thriving, notably in the top habitats. These outcomes highlight the importance to focus investigations not selectively on a single habitat type or depth zone in order to properly assess MPA effectiveness. Consequently, the monitoring and protection of fish species supported by marine spatial planning may benefit from an improved understanding of ecological functioning provided by MPA performance.