When last assessed in 2010, the IUCN Red List categorized Magellanic penguins as near threatened. While an overall moderately rapid decrease is apparent, some smaller colonies of penguins have grown. During their annual migrations, penguins would often drift into shipping lanes and get oiled. However, changes to the Chubut provisional law moved the designated lanes to reduce oiling incidents. Magellanic penguins are also unintentionally caught in fishing nets and die as a result. Through commercial fishing humans are depleting populations of small fish which are a main component of Magellanic penguins' diets. The IUCN has proposed reducing by-catch of an anchovy fishery in Argentina and monitoring the effects on a penguin population in Punta Tombo as a possible solution.

CITES: no special status

IUCN Red List of Threatened Species: near threatened