Just thirteen days after founding Mission San Jose Father Lasuen founded Mission San Juan Bautista. Located in the middle of the San Juan Valley, the mission sits right on the San Andreas Fault! Although its location right on the fault was less dangerous than other locations, it accounted for many shaky days and nights. In October 1798 the shaking was so bad that the missionaries slept outside for the whole month. The earth shook as many as 6 times on one day, leaving many huge cracks in both the buildings and the ground.

Since the mission population was growing so quickly, when an earthquake destroyed the church in 1803 plans were already underway to build a larger church. Unlike most churches that were long and narrow with a single center aisle, this was to be wide enough for three aisles and room for over a thousand people. However, before the church was complete the padres became concerned that such a large structure would be unsafe in an earthquake. They felt that the open-arched walls separating the two side aisles were not strong enough to support the large tile roof when the ground shook.

Except for the first pair, all the arches were closed up to provide a safer structure. Thomas Doak, a sailor from Boston who jumped ship in Monterey, thereby becoming the first, painted much of the interior Anglo-American resident in California. Although he was not a great artist, he did work for just room and board, and the colors he mixed were so durable that they continue to glow today.

Among Father Arroyo's many talents was his ability to preach to the Native Americans in seven of their dialects. After rheumatism confined him to a chair he created the first dictionary-like document of the native languages.

Father Tapis who retired there after serving nine years as Father-President of the California missions. Like Father Duran at mission San Jose, Father Tapis was also very musically inclined. He created a system of using different colors for different types of music notes that made it much easier for the natives to follow. His choir of Native American boys was famous and performed for many visitors.

After secularization in 1835 the church continued to serve as a parish for the local town. After sustaining some damage from a quake in 1906, it was repaired and then suffered through some attempts at modernization. Fortunately, in 1949, the Hearst Foundation financed the restoration that restored it to its original form.

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