The Iglesia de San Isidro is the older of the two churches located at Gran Quivira. Constructed from local limestone between 1630 and 1635, this church is 109 feet long and 29 feet wide. Its design closely resembles that of the church at Abó. There is a walled cemetery, known as a campo santo, situated just to the east of the church.
After Gran Quivira was abandoned, the Iglesia de San Isidro attracted many treasure hunters. In the 1930s, Jacobo Yrisarri dug a deep shaft in the church's apse and created a tunnel leading to the San Buenaventura Church. Frank "Boss" Pinkley, the Superintendent of the Southwest National Monument, reported entering the treasure shaft before it was sealed in 1940.
The first excavation and stabilization of San Isidro took place in 1951, led by NPS archeologist Gordon Vivian. The Salinas Pueblo Missions continues to work on stabilizing the structure approximately every five years.