For more than three centuries – from the late 1100s to 1580 – Puye Cliffs was home to 1500 Pueblo Indians who lived, farmed and hunted game there. In the late 1500s, Puye Cliffs’ inhabitants moved into the Rio Grande River valley, likely due to drought that caused springs to dry up and crops to fail. Puye Cliffs’ inhabitants are ancestors of the present-day Santa Clara people, who now live at Santa Clara Pueblo, ten miles east of Puye.
Puye Cliffs consists of two levels of cliff dwellings cut into the cliff face, as well as dwellings on the mesa top. The first level is over one mile long and runs the entire length of the base of the mesa. The second level is about 2,100 feet long. Stairways and paths were cut in the face of the rock to connect the two levels and to allow people to climb to the top of the mesa. Dwellings on the mesa top are examples of Pueblo architecture and were part of a single, multi-storied complex built around a large, central plaza. The complex is known as the Community House or Great House. While the actual number of rooms is unknown, the south part of the complex had 173 rooms on the ground floor, with multiple stories in various places, similar to modern-day Taos Pueblo.

The largest of all settlements in the Pajarito Plateau, Puye Cliffs was excavated in the summer of 1907 by Edgar Hewitt, in cooperation with the Southwest Society of the Archeological Institute of America. It was the first of the ancient Pueblos of the Rio Grande Valley to be systematically excavated, and was named a National Historic Landmark in 1966.

Geologically, the Pajarito Plateau was formed from successive layers of basalt and volcanic tuff created by eruptions of the Jemez Caldera volcano. Over time, erosion by rain, snow, wind and cycles of freezing and thawing carved through the tuff to form sheer cliffs that border the canyons of the Jemez Mountains. The weathering of the cliffs created a somewhat hard surface layer that could be easily broken, with a soft and crumbly underlying tuff that could be dug away by stone tools.

Beginning in the late 1100s, the upland mesas flanking the east side of the Jemez Mountains were settled by people of the Anasazi Culture. At first there were hundreds of individual, family-size dwellings, but by A.D. 1300, the people were converging in relatively few principal villages which grew to considerable size. Such villages include Puye, Tsankawi, Tyuonyi, Otowi, Shufinne, and Tsirege. The latter village, Tsirege, means "little bird" in the Tewa language. Archaeologist Edgar L. Hewett adopted the name, but translated it into Spanish - Pajarito - and applied it as a general name for the great area of prehistoric settlement around the eastern flanks of the Jemez Mountains, thus the Pajarito Plateau. All settlements of the Pajarito Plateau contain cliff dwellings and Great Houses, or large, multi-storied dwellings arranged around central plazas. With 1500 inhabitants at the height of its occupation, Puye Cliffs is the largest of all settlements in the Pajarito Plateau.

Harvey Houses were built by the legendary Fred Harvey Company in the late 1800s as amenities for tourists traveling to the Southwest by railroad, and later, and passenger car. The Harvey House at Puye Cliffs is the only Harvey House built on an Indian reservation.
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