The church has been through a lot in it's history. The first temporary church, built in 1797, burned down in 1806 and the new church was not built until 1821. In 1834 the mission was secularized after Mexico won independence from Spain, and the mission was put under civilian control. During that time commercial businesses moved into some of the rooms. One of them was even a saloon.
In 1859, President Buchanan returned the mission property to the Catholic Church, but the Franciscan Friars did not regain the administration of it until 1928. The church was severely damaged in the December, 2003, earthquake, and was not able to reopen for six years -- after renovation had taken place. The church held its first service after the earthquake on September 29, 2009. The church remains in use today and is accessible to visitors. I will show you the interior in my next post.
To learn more about the California Missions, I recommend one of these books.
California MissionsThe California Missions Source Book: Key Information, Dramatic Images, and Fascinating Anecdotes Covering All 21 Missions (Essential Facts at a Glance)The California Missions: A Complete Pictorial History and Visitor's Guide (Sunset Pictorial)California Missions: The Earliest Series of Views Made in 1856