Implementing effective conservation measures to manage migratory populations is challenging, especially in a relatively inaccessible dynamic environment such as the ocean. With limited financial and human resources, efforts must be intelligently prioritized to achieve conservation success and reduce uncertainties of conservation efforts. The southwest Indian Ocean (SWIO) hosts some of the world’s most important breeding grounds for the Critically Endangered hawksbill turtle Eretmochelys imbricata. However, knowledge gaps remain about the movement patterns of this species. Between 2007 and 2022, we deployed 17 satellite tags onto hawksbill turtles from scattered locations in the SWIO: 16 nesting females—Granitic Islands, Seychelles (n = 9); north Madagascar (n = 5); Moheli, Comoros (n = 1); Juan de Nova, Terres australes et antarctiques françaises (n = 1)—and 1 female bycaught in fisheries (east Madagascar). We found strong variability in migratory movements amongst individuals, particularly in terms of distance and movement persistence. Detailed analysis of movement persistence reveals that these individuals behave differently in neritic and oceanic habitats, with a lower movement persistence in neritic habitats. We identified a total of 12 foraging areas scattered throughout the SWIO, both in coastal and open-sea neritic habitats. These results reinforce the need to consider the importance of neritic habitats, for both migration and foraging, in conservation policies. The quantification of the degree of migratory variability is particularly important to developing conservation plans and strategies at both the national and international level, including the delineation of regional management units (RMUs) in the Indian Ocean.