The site was home to some 1500 pueblo Indians from about the 12th century until 1577 when drought finally forced the villagers to leave for locations nearer to the Rio Grande. Oral tradition suggests that the present day inhabitants of Santa Clara Pueblo, some 10 miles (16 km) to the east, are the descendants of Puye.
The dwellings are remarkable for being carved out of a 200 ft (61 m) high (60 m), cliff ridge formed from volcanic tuff. The rock is relatively soft and can be excavated using wooden tools. Some 740 rooms are carved out of the cliff, although foundations show that additional houses constructed from talus blocks lined the base of the cliff. In fact it seem likely that many of these houses grew to be several stories high and the cave rooms were then just the back rooms of these homes.
Along with the cave rooms, lines of post holes are carved into the cliff face. These would have supported roof beams for the block house and may also be anchor points for wood ladders and walkways used to reach the cliff houses. There are also about a dozen stairways, more like ladders of foot and hand holds, that lead to the top of the cliff. Many of the stairways lead up to the large 'Community House' which has been partly reconstructed on the top of the cliff.