Mission San José established the settlement that became the modern city of Fremont. It was the first of a group of five approved as part of a major expansion of the Alta California mission system.

The expansion was intended to reduce the distance between missions, and the need for military escorts when travelling between the missions. The rich lands around the mission were very productive, and it helped to supply livestock, fruit, grain, and olive oil to the surrounding missions.

The mission was, however, troubled by unrest between the Indians and the missionaries. A large-scale Indian uprising in 1828 required over a year, and several military expeditions from the Presidio at San Francisco, to quell.

Plans for a bell tower at the mission were scrapped due to fear of earthquakes. In fact, the mission church and most of the other buildings were destroyed by a major earthquake in 1868.

A new Adobe church was constructed in 1890, but evenutally fell into ruin.

In 1981, a reconstruction of the 1890 adobe church was begun, partially funded by San Francisco Bay Area philanthropist Walter Gleason.  The work was completed in 1985.

The reconstruction used historically accurate materials and construction techniques wherever possible; however, the new structure has an earthquake-resistant steel core.  The current structure is considered to be a near-perfect replica of the original church.

In 1986, an organ was added to the church.  The organ, called the Opus 14, was built by Rosales Organ Builders, Inc. of Los Angeles.  It is based on the design of Spanish organs of the 18th century, although neither Mission San José, not any of the other Spanish missions, had originally had an organ.  The mission was painted in bright colors typical of the “Greco-Roman Revival” style of the 1830s, and fits well with the church.