Marine protected areas can serve to regulate harvesting and conserve biodiversity. Within large multi-use MPAs, it is often unclear to what degree critical sites of biodiversity are afforded protection against commercial activities. Addressing this issue is a prerequisite if we are to appropriately assess sites against conservation targets. We evaluated whether the management regime of a large MPA conserved sites (Key Biodiversity Areas, KBAs) supporting the global persistence of top marine predators. Location: Southwest Atlantic Ocean. We show that current fishery management measures within the MPA contribute to protecting top predators considered in this study and that resource harvesting within the MPA does not pose a major threat—under current climate conditions. Unregulated fisheries beyond the MPA, however, pose a likely threat to identified KBAs. Our approach demonstrates the utility of the KBA guidelines and multispecies tracking data to assess the contributing role of well-designed MPAs in achieving local and internationally agreed conservation targets.