Although it was an early penguin, Inkayacu closely resembled its modern relatives. It had paddle-like wings with short feathers, and a long beak. Inkayacu, along with other extinct penguins from Peru, are often referred to as giant penguins because of their very large size. Inkayacu was about 1.5 metres (5 ft) long, in contrast to the largest living penguin, the Emperor Penguin, which is about 1.2 metres (4 ft) long.
The melanosomes within the feathers of Inkayacu are long and narrow, similar to most other birds. Their shape suggests that Inkayacu had grey and reddish-brown feathering across its body. Most modern penguins have melanosomes that are about the same length as those of Inkayacu, but are much wider. There is also a greater number of them within living penguins' cells. The shape of these melanosomes gives them a dark brown or black color, and is the reason why modern penguins are mostly black and white. Despite not having the distinctive melanosomes of modern penguins, the feathers of Inkayacu were similar in many other ways. The feathers that made up the body contour of the bird have large shafts, and the primaries along the edge of the wings are short and undifferentiated.
Fossils of Inkayacu were first found in 2008 on the Pacific coast of Ica, Peru. A nearly complete skeleton was uncovered in the Paracas National Reserve by an expedition team led by Rodolo Salas and studied by a team led by Julia Clarke of the University of Texas. Large penguins, including the species Perudyptes devriesi and Icadyptes salasi, had been described from the area the previous year. The first evidence of melanosomes is fossilized feathers was published in late 2008, being reported from an Early Cretaceous bird. Paleontologist Jakob Vinther, an author of the 2007 paper on the first fossilized melanosomes known, found melanosomes in the feathers of Inkayacu soon after the fossil was discovered.