Mission San Jose was founded in 1720 at the urging of Father Margil de Jesus, with the approval of the Marques de Aguayo. Over 104 years as a mission, more than 2,000 Native people were baptized here. It was fully secularized on February 29, 1824.
Construction of the limestone church began in 1768, when about 350 Native residents lived in 84 two-room apartments. After visiting in 1777, Father Morfi called it the Queen of the Missions, and the church was finished around 1782.
The Rose Window is called an outstanding example of Spanish Colonial decoration, but no one knows who carved it. The granary was finished around 1755, and the grist mill ran from 1794 to 1809 and was restored in 2001. The missions became a UNESCO World Heritage Site in 2015.

