Six years after the founding of the thirteenth mission in Soledad Father Lasuen was granted permission to establish 5 additional missions, which he did in just 13 months. Mission San José was the first of these. Father Lasuen's plan was to locate the missions within one day's travel of another to be used as a safe rest stop for those traveling along the El Camino Real.

Located east of the San Francisco Bay, Mission San José was in a troublesome location known to be an area populated with many runaway neophytes (Christianized Native Americans) and hostile tribes. It served as a base for military operations against those Native Americans resentful of the intrusion of the missionaries. Many skirmishes and battles took place here between the hostile natives and the Spanish soldiers.

As a result of these difficulties conversions were slow. In the first year only thirty-three Native Americans were baptized. But eventually Mission San José had more converts than any other mission in Northern California. Over 6,000 baptisms were recorded.

The fertile land was well suited for large agricultural outputs of fruits, wheat and corn. They also had over 20,000 heads of cattle and sheep.

Much of the prosperity of this mission is due to Father Narciso Duran who presided over the mission for 27 years before he went on to become the Father-President of the California missions. Frey Duran had a great talent for music and taught many neophytes (Christianized Native Americans) how to read music and play the many instruments he obtained from Mexico. He even created a thirty-piece band whose mission concerts drew audiences from many miles away.

A large adobe church was built for the many converts at Mission San José and it stood until a violent earthquake in 1868 destroyed it. In 1869 a wooden gothic-style church was erected on the foundation of the old church. It served as a Catholic parish until 1965. In 1982 it was carefully relocated to a town called Burlingame.

In 1985 one of the most authentic restorations of all the California missions was completed in Mission San José. Authentic adobe bricks were used and most of the work was done with tools resembling those used at the time of the original mission building.