Mission San José was found on(June 11), 1797 on a site located in the "Mission San Jose District" of Fremont, California (formerly an independent town, a spot that the natives called Oroysom or Orisom) in the "Valley of San José." The settlement was the site of the first Ceasarian section childbirth in Alta California. The Mission entered a long period of gradual decline after secularization in 1834, though numerous restoration efforts in the intervening periods have reconstructed many of the original structures. The original padre's quarters are now a small museum; Saint Joseph's Church at the Mission San José is today a local parish church of the Diocese of Oakland. The church has a regular Mass schedule and also has a visitors' center, museum (open daily) and slide show telling the history of the Mission.
In the early part of the 1900s a sign was erected on the roof of the museum which read "Mission San Jose de Guadalupe" (in reference to el pueblo de San José de Guadalupe, the first civic settlement in Alta California, founded in 1777 ). Regrettably, this misnomer is often used by authors and even government agencies to this day when referring to the installation.
Father Narciso Durán became the pastor of the mission in 1806, and remained until he was replaced by Father José González Rubio in February 1833 as part of a post-independence policy requiring the replacement of Spanish-born clerics with those born in Mexico. Durán trained the neophytes in music, organizing both a choir and a 30 piece orchestra that became famous throughout California. While at San José, Father Durán twice served as Father-Presidente of the Franciscan missions.
The Mission's permanent adobe church was dedicated with great ceremony on April 22, 1809. Valuable gifts of vestments, sacred vessels, religious statues, and paintings attested to the generosity of friends of the Mission in the Bay Area and abroad. The majority of vestments in the modern collection date from the late 18th and early 19th centuries. The silken fabrics and embroideries were products of various textile centers of the Spanish Empire, whose suppliers extended from Europe to Asia. Mission San José was the center of industry and agriculture. The site was chosen for the abundance of natural resources of the area including water, fertile ground, stones, and adobe soil suitable for building. Thousands of cattle roamed the Mission ranges, and acres of wheat and other crops were planted and harvested under the direction of the padres. In 1810, it produced 4,070 bushels (110 metric tons) of wheat and much produce, including grapes, olives, and figs.
In 1832, the Mission's 12,000 cattle, 13,000 horses, and 12,000 sheep roamed Mission lands from present-day Oakland to San Jose. San José was one of the most prosperous of all of the California missions. An 1833 inventory prepared by Father José González Rubio lists a church, monastery, guardhouse, guest house, and a women's dormitory, in addition to the thousands of acres of crops and grazing land. This prosperity was not to last long, however. On August 17th of that year, the Mexican Congress passed An Act for the Secularization of the Missions of California.
The original mission complex consisted of over 100 adobe buildings. Restoration efforts by the Native Sons and Daughter in the West in 1915 and 1950 saved the surviving portion of the Mission wing and converted it into a museum, set in the gracious surroundings of flowers and palm trees. In 1956, the town of Mission San José incorporated with four others to become the City of Fremont. Plans to reconstruct the church of Mission San José were launched in 1973. The Victorian-style rectory was relocated to nearby Anza Street and the Gothic-style wooden church was moved to San Mateo where it has been restored as a house of worship by an Anglican church group. After extensive archaeological excavations and planning, construction began in 1982 on a replica of the 1809 adobe church. Work was completed and the facility rededicated on June 11, 1985. The walls vary in thickness from 4 to . Old timbers and rawhide thongs demonstrate the practicality of the padres who, having no iron nails for building, substituted the leather laces. Consequently, the lumber used in the reconstruction has been given a hand-hewn appearance.
With its "simple and forthright" exterior, the Mission church stands as a tribute to those whose efforts made this dream come true. The richly decorated interior follows the descriptions in the historic inventories of the 1830s. The crystal chandeliers are copies of period pieces similar to ones listed in the old church inventories. Two of the original statues have been placed on the two side altars. Ecce Homo, a figure of Christ clothed in a scarlet robe and crowned with thorns, stands on a balcony above one of the side altars. The other statue of Saint Bonaventure was carved from wood and then painted. The original baptismal font of hammered copper on a turned wood base has been returned to the church, as has the bell wheel used by the Ohlones during the sacred parts of the Mass.
The reredos behind the main altar features a painting of Christ, a statue of Saint Joseph, and two carved figures: a dove represents the Holy Spirit, and at the top sits God the Father with beautiful golden rays surrounding him. The altar and choir railings were copied from an original piece found in the museum during the reconstruction. The Mission cemetery (camp santo) is situated to the side of the church where a great number of Mission pioneers buried. During the dig, the marble grave marker of Robert Livermore was located in the original tile floor of the church. It was carefully repaired and replaced in the reconstructed church. Many prominent Spaniards are buried in the floor of the Mission church but only Livermore's grave is marked. Thousands of Ohlones are resting in the Ohlone cemetery located about a quarter of a mile from the mission down Washington Boulevard. Three of the original Mission bells were transferred from the destroyed adobe church to the wooden church of 1869, where they hung until the 1970s. The fourth bell had been given to a church in Oakland and recast, but was returned to the Mission during the reconstruction of the bell tower. Now all four bells are hung, ready to ring on special occasions.
In 1985, restoration of the church was completed by the Committee for the Restoration of the Mission San Jose and the Catholic Diocese of Oakland. It is considered to be a near-perfect replica of the original church, though it incorporates a concealed structural steel frame which provides earthquake resistance. Further reconstruction of the missing part of the padres' living quarters and a restoration of the surviving adobe wing are part of the overall plans for the Mission. Today, the Mission is administered by St. Joseph's parish, which includes the Mission building and the surrounding areas, an ordinary church building used to fulfill the daily needs of the parish, and a school serving students in grades 1-8.