Mission Santa Cruz sits on a gentle slope surrounded by the beautiful redwood trees not far from where they meet the Pacific Ocean. When Father Lasuen raised the cross and said Mass on this picturesque location, little did he realize the misfortune and troubled times that would befall the mission.

Having experienced problems in the past when the missions were located too close to another settlement, the Franciscans saw to the passing of a law requiring at least a league of land between the mission and a pueblo (town). In Santa Cruz the Governor ignored this law, and even before the mission quadrangle was complete, notified the padres that not only was there to be a pueblo nearby, but that they would have to help support it. The padres tried to stop the founding of the Branceforte pueblo, but to no avail.

Many of the settlers that arrived from Guadalajara were criminals, with no ambition to grow their own crops. They often raided the mission's crops and would go out of their way to antagonize the natives.

On a day in 1818 the pirate Bouchard was spotted off the coast. The missionaries were aware of Bouchard's earlier attack on the Monterey Presidio (fort), so along with the neophytes (Christianized Native Americans), they quickly retreated inland to the safety of Santa Clara. When they returned they found that the mission had been plundered, but not by the pirate Bouchard. The Branceforte pueblo residents had helped themselves to everything of value at the mission.

Because of the unruly settlers in Branceforte the padres found it necessary to keep a very tight rein on the Native Americans, severely restricting their movements. This contributed to the fact that Mission Santa Cruz had the lowest population of all the California missions. Some of the neophytes behaved badly under such strict confinement, and many believed that they were treated too cruelly. This eventually led to the murder of one of the padres that was later to be the cause for the first autopsy performed in California.

Mission Santa Cruz was one of the first to be secularized. The land and supplies were sold and the few remaining natives left. Two earthquakes, in 1840 and 1857, destroyed the mission church. In 1889 a white painted brick church was build in its place for use by the town. In 1931 a small replica of the original mission church was built near the original site.