The main unit of the park preserves the ruins of Pecos Pueblo, known historically as Cicuye (sometimes spelled Ciquique), the "village of 500 warriors".

Within 350 years the Pueblo IV Era Pecos village had grown to house more than 2,000 people in its five-storied complex.

Farming was a main part of their diet and staple crops included the usual beans, corn, and squash.

Their location, power and ability to supply goods made the Pecos a major trade center in the eastern part of the Puebloan territory, connecting the Pueblos to the Plains cultures such as the Comanche.

A 1.25-mile (2 km) self-guiding trail begins at the nearby visitor center and winds through the ruins of Pecos Pueblo and the mission church.

A traditional kiva was built in front of the church during the Pueblo Revolt in 1680 as a rejection of the Christian religion brought by Spanish colonists.

Confederate forces were en route to take Union-controlled Fort Union, and were fought to a standoff by militia raised in the New Mexico and Colorado Territories.

In 1965, President Lyndon Johnson established Pecos National Monument over the same area, and control was turned over the Park Service.

In 1990 the main unit of the park was expanded to more than 6,000 acres (24 km2), including a large area of ranchland and archaeologically sensitive landscapes.