Father Antonio Cruzado designed the mission and it has several unusual characteristics. It is the only mission with Moorish style architecture, and the front of the building is actually a side wall. The design may have been based on the Cathedral of Cordova in Spain, which was once a Moorish mosque. It is also built from stone, brick and mortar, unlike most other missions that were built from adobe.
It took 26 years to build the church, from 1779 until 1805. The church is 150 feet long and 27 feet wide, with walls 30 feet high and five feet thick. It will hold about 400 people.
An earthquake in 1812 destroyed the bell tower and damaged the father's quarters. They lived in the granary until repairs were made. Restoration took until 1828 and the bell tower and it was replaced with a bell wall, or campanario. There are six ancient bells in it.
The mission is one of the best preserved, with many of its original features still intact, including a hammered copper baptismal font, a gift from King Carlos III of Spain in 1771, and six altar statues brought around the Horn of Africa in 1791. The altar was made in Mexico City and brought to the mission in the 1790s.