The site was a military fortress designed to protect the city of Cusco and served as a settlement. Scholars believe it was an Incan administrative center of sorts. There are aqueducts, plazas, baths, fountains, and other signs that reflect its non-military uses.
The Inca Trail also passes right by Puka Pukara. As a result, visitors may have used the site as refuge along the journey.
There are tunnels on site and there is speculation that they once led to the “Incan Spa” of Tambomachay.