This was the mission established furthest south on the peninsula during colonial times.

It was founded in the location that the Pericúes called Añuití, which is now part of San José del Cabo.

The mission was dedicated to Saint Joseph, funded by the Marquis of Villapuente de la Peña, and built by Father Nicolás Tamaral and the visitor José de Echeverría. This was the fourth mission on the peninsula.

Initially, the mission was built of adobe near the beach, and later it moved eight kilometers inland from the coast.

In 1734, the Mission was the scene of the Pericú Rebellion, resulting in Tamaral's assassination and the destruction of the mission.

Between 1735 and 1736, the headquarters were moved back near the coast, but with the status of a Visit of the Añiñí mission. Additionally, a Spanish presidio was established nearby. 

In 1753, the mission was moved further inland again, and due to the expulsion of the Jesuits, Añuití came under the custody of the Dominicans.

In 1793, the construction was damaged by a flood and was rebuilt in 1799. In 1822, the Chilean ship "Independencia" attacked the plaza, causing serious damage to the mission once again until it was finally abandoned in 1840.

The current church was built in 1940, very close to the original site where the old Jesuit mission was erected.

One notable feature on its façade is a mosaic depicting the assassination of Father Tamaral by the Pericúes who inhabited the region. The building is surrounded by a pleasant colonial-style plaza.