This mission has undergone several name changes. 

Initially, it was called the Visit of the Pericú territory. Later, it was named Mission of Santa Rosa de la Ensenada de Palmas, Mission of Santa Rosa de Todos los Santos, until it became known as Mission of Todos Santos.

When it was considered a Visit, it consisted only of a small adobe chapel built by the missionary Father Jaime Bravo, who also had an orchard to supply the Mission of Our Lady of Pilar de la Paz de Airipí.

In 1726, the Visit was abandoned, and in 1733, the mission was founded by the missionary Segismundo Taraval. Funding was provided by the Marquis of Villapuente de la Peña, and it was then named Mission of Santa Rosa de la Ensenada de las Palmas.

In 1749, due to water scarcity, the missionaries had to abandon the Mission of Our Lady of Pilar de la Paz de Airapí and relocate to Mission of Todos Santos.

By 1767, epidemics and rebellions had significantly reduced the population, so the few survivors were sent to the Mission of Santa Rosa in the town of Todos Santos, and it was precisely during that time that the mission was known by the name of the town.  y las rebeliones habían mermado de forma importante la población, por lo que los pocos sobrevivientes fueron enviados a la Misión de Santa Rosa en el poblado de Todos Santos y fue justamente en esa época cuando la misión fue conocida con el nombre del poblado.

The mission closed its doors to religious worship in 1840, and it was not until the mid-20th century that the old mission was renovated. Today, it is known as Our Lady of Pilar de Todos Santos.