We studied the migration of Magellanic penguins near the southern tip of the breeding distribution, and for the first time found evidence of partial migration for this species within the same colony. Forty‐three percent of the penguins studied stayed within ~ 290 km of the colony (residents), while others went northwards as far as 2000 km. All penguins spent the same amount of time at sea and traveled similar total distances, but residents experienced colder waters (2°C lower) and habitats with lower Chlorophyll‐ a concentrations than migrants. The two habitats are inhabited by different prey items, consequently offering the penguins distinct prey options. We have shown high variability in the non‐breeding dispersion behavior of Magellanic penguins within the same colony; nonetheless, further research is required to understand the proximate and ultimate causes, and the consequences, of this behavior.