Recent meta-analyses identified conservation hotpots at the scale of the Mediterranean, yet those may be crude by lack of detailed information about the spatial ecology of the species involved. Here, we identify an irreplaceable marine area for >95 % of the world population of the Scopoli’s shearwater (Calonectris diomedea), which is endemic to the Mediterranean and breeds on the island of Zembra off Tunis. To this end, we studied the three dimensional at-sea movements of 50 breeding adults (over a total of 94 foraging trips) in 2012 and 2013, using GPS and temperature–depth recorders. Feathers were also collected on all birds to investigate their trophic status. Despite Zembra being the largest seabird colony in the Mediterranean (141,000 pairs), the per capita home-range of Scopoli’s shearwaters foraging from this colony was not larger than that of birds from much smaller colonies, indicating highly beneficial feeding grounds in the Gulf of Tunis and off Cap Bon. Considering depleted Mediterranean small pelagic fish stocks, supposed to be Scopoli’s shearwater prey base, we therefore speculate that birds may now also largely feed on zooplankton, something which is supported by our stable isotopic analyses. Crucially, shearwater at-sea feeding and resting areas showed very little overlap with a conservation hotspot recently defined on the western side of the Gulf of Tunis using meta-analyses of species distributions relative to anthropogenic threats. We therefore propose a major extension to this conservation hotspot. Our study stresses the importance of detailed biotelemetry studies of marine megafauna movement ecology for refining large-scale conservation schemes such as marine protected area networks.