San Jose was one of the most successful missions in the chain but it was a troublesome spot. Runaway neophytes from Mission Dolores hid in this area. The local tribes were known for their fighting spirit. The mission was often used as a base for military expeditions.
The mission was protected by a small group of soldiers (on average five were stationed at each mission) but as noted above this permanent contingent was augmented by soldiers from the presidio (fort) in San Francisco.
The mission was famous for its music. Under the leadership of Father Narcisco Duran (who later became Father President of the mission chain) the mission had a thirty piece band and renowned choir. Concerts at the mission attracted people from all over.
San Jose was also the site of a large Indian uprising (1827) under the leadership of a neophyte from San Jose, an Indian named Estanislao (Stanislaus County is named after him).