[5] Humboldt penguins nest on islands and rocky coasts, burrowing holes in guano and sometimes using scrapes or caves.

[15] Most penguins moult between mid-January and mid-February, however the initiation varies with latitude and favourable conditions such as food abundance.

It is known in Peru as the pajaro-niño, which translates to "baby-bird", due to their waddling gait and flightless wings held out suggesting the image of an infant toddling on the beach.

[18][21] The Humboldt penguin's breeding distribution ranges from southern Chile along the dry and arid coastal regions of the Atacama Desert to subtropical Isla Foca in north Peru.

Its range is restricted to the coast and offshore islands affected by the Humboldt current, which provides a continuous supply of nutrients and food, thus supporting huge populations of seabird.

[18] In July 2002, a Humboldt Penguin was caught in a fishing net off the coast of Prince of Wales Island in Alaska.

[31] In the ecstatic display to attract a partner, the bird extends its head vertically, collapses its chest, flaps its wings and emits a loud call resembling the braying of a donkey.

[17] The Humboldt penguin lay eggs from March to December, but also with peaks in April and August–September, due to individuals having a second clutch.

[31] Nests of the Humboldt penguin can also be found at caverns, hollows, cliff tops, beaches and scrapes covered by vegetation.

During the El Niño, upwelling of nutrient-rich bottom water in the south-eastern Pacific Ocean is depressed, as well as sea surface temperature anomaly (SSTA) value increases.

[21] The estimated energetic demands of the total Humboldt penguin population during breeding season sums up to 1,400 tons of fish.

[9] Humboldt penguins need up to half an hour to recover to normal heart rates after human approach, however, this time decreases with repeated visitation.

[7] The feral goats browse the vegetation the penguins use to build their nests and they can lead to collapse to dirt burrows.

[37] Some Humboldt penguin colonies face emerging pressures from industrial development; the construction of coal-fired power plants and mining proposals in Chile.

In 2017, Andes Iron proposed to construct a mineral export port near the Humboldt Penguin National Reserve in Chile's Coquimbo region.

[40] Andes Iron challenged the decision,[41] and environmental approval for the Dominga mine and Cruz Grande port project was eventually granted.

Oceana has since challenged the proponents compliance at the work site and as of 2020 continues to lobby for the abandonment of the project and protection of region's rich marine biodiversity.

[42] If constructed, the Dominga complex will include an open pit copper mine, processing facility, desalination plant and port.

[43] The historical breeding grounds for the Humboldt penguin were guano layers which covered islands of the Peruvian and northerly Chilean coasts in which the birds could burrow.

[31] The guano, a rich fertiliser and source of income for the Peruvian Government, and eggs of the Humboldt penguin were regularly sought after.

[20] The decline of the Humboldt penguin population is attributed to the harvest of guano in the 1800s, which led to the destruction of breeding grounds and to human disturbance.

[34] The combination of an environment changed by human developments as well as the long duration and strong intensity of the event that year led to major effects on the fecundity and survival of the Humboldt penguins.

[34] Humboldt penguins were given legal protection in 1977 by the Peruvian Government and listed in Appendix I of the Convention of International Trade of Endangered Species (CITES).

[45] It is categorised as vulnerable due to extreme population size fluctuations, clustered distribution and the major threats to the species not being ameliorated over time.

[46] Peruvian legislation categorises the species as endangered and prohibits the hunting, possession, capture, transportation and export of the bird for commercial purposes.

[46] In 2017 a large mining project proposed by the company Andes Iron in Chile was vetoed due to the possible environmental impact on the penguins,[48] though that decision was subsequently overturned.

Historically, the Humboldt penguin population was impacted by the extraction of guano from their breeding colonies, which reduced the available habitat for burrowing and nesting.

[58] In 2009 at the Bremerhaven Zoo in Germany, two adult male Humboldt penguins adopted an egg that had been abandoned by its biological parents.

A further example of this kind of behavior came in 2014, when Jumbs and Kermit, two Humboldt Penguins at Wingham Wildlife Park, became the center of international media attention as two males who had pair bonded a number of years earlier and then successfully hatched and reared an egg given to them as surrogate parents after the mother abandoned it halfway through incubation.