Named for Crusader Saint John of Capistrano and designed in the shape of a cross, the great stone church once held seven domes and a bell tower so tall it could be seen from ten miles away. Severely damaged by an 1812 earthquake, the ruins are currently being preserved by archaeologists and engineers. Ivy covers the broken walls, willows sway over the fountain in the quadrangle and orange Birds of Paradise grace the mission gardens.

A gilded altarpiece illuminates the Serra Chapel of 1777, the oldest building still in use in California and the only surviving church where Father Serra said mass. Each year on St. Joseph's Day, March 19, the mission celebrates the return of the cliff swallows from Argentina with a traditional Mexican fiesta.