Mission San Juan Capistrano was established in 1731 and underwent several building periods. The complex has the traditional plan of buildings and walls surrounding a central courtyard and includes the ruins of the second and third church, the foundations of some of the residential quarters, a convento (missionary quarters), granary foundation, well, and a residence.

The Mission at San Ildefonso became the center of Franciscan activity in the north when first built. The church was burned down in the Indian revolt of 1696 and then rebuilt later by the Spanish. The new church remained practically unaltered until 1905, when several substantial alterations were made and the church was nearly entirely rebuilt.