In 1827, the mission quadrangle was completed, with sides 900 feet long. The inner patio was surrounded on three sides by buildings and by a ten foot high wall on the fourth side. Normally, the mission church was in the corner of the quadrangle, but at Mission San Jose it was in the center of the front side. There was a soap factory and a tannery here, and a hot water fountain from the nearby hot springs was used for bathing. The Indians' adobe homes were behind the quadrangle along with a kitchen garden, orchard and vineyard.

In 1868, an earthquake damaged the adobe church, breaking open the roof, breaking one of the bells and destroying the mission walls. The broken bell was repaired and used by a church in Oakland. In 1890 a wooden church was built on the old foundation. The three unbroken original bells were used until 1970 when the tower holding them became unsafe and they were stored.

Finally, in 1973 a committee was formed to restore Mission San Jose. The wooden church was moved away and the first part of the restoration was completed in 1985. The reconstructed mission looks like it did after it was redecorated, duringi the years 1833-1840. A few items from the original mission remain. The fourth bell was returned and all were rehung in 1984. The original copper baptismal font, decorated by the famous Mexican artist Augustin Davila survived the earthquake. It sits on a wooden stand that he also decorated.