According to the IUCN, the main threats to the species include biological resource use, human intrusions and disturbance, invasive species, diseases, and pollution. The organization notes fisheries may be a threat because the penguins can be incidentally captured in fishing nets in addition to competing for resources humans are after as well. There is also concern about increasing oil exploration around the Falkland Islands, which is also home to gentoo penguins, as well as pollution from oil spills.
Harmful algal blooms and diseases have also affected populations in the past. Meanwhile, human tourism has been caused decreased breeding productivity. Experts are also worried about penguins and other Antarctic animals are ingesting plastic particles from sources thousands of miles away, highlighting the need to study the levels of microplastics in the areas where the animals live. The same issue is also affecting ecosystems at the other pole in the Arctic.