The Magellanic penguin (Spheniscus magellanicus) is a top predator and a major consumer of marine resources in the Patagonian Continental Shelf and worldwide. It is the most highly migratory of the Spheniscus penguins, but until recently, its migration route was only partially known. Regarding Magellanic penguins breeding on Isla Quiroga, in Argentina, our goals were: (1) to compare distribution during winter period between sexes and (2) if habitat is found to be segregated, to evaluate possible proximate causes like competitive exclusion and/or habitat specialization. In March 2017 and 2018, prior to migration, 26 penguins were equipped with MK3/4 geolocators, which were recovered in late September/early October. Penguins dispersed northwards as far as 29°S and southwards up to 56ºS, near the Beagle Channel, distributing over a 2158 ± 50 km latitudinal range and showing a large-scale distribution pattern across longitudes on the continental shelf. We found a longitudinal segregation between sexes in winter grounds, with males closer to the 200-meter isobath and further from the coastline than females. Morphological and physiological differences between sexes might allow males to dive deeper than females at a lower cost, which could result in a more offshore path for males. This spatial segregation was supported by bulk blood stable isotope values and estimated isotopic niche, which showed differences between males and females upon arrival from winter breeding grounds, but not while penguin bred and behaved as central place foragers in the colony. For the first time for this species, we combined two independent tools, geolocation and stable isotope data, and found that sexual segregation in habitat use could potentially generate an optimal winter foraging strategy for each sex, precluding potential intersex competition for food.