The mission was dedicated to Francis Xavier, a Navarrese Catholic missionary and saint who was a co-founder of the Society of Jesus.
The Jesuits were told by Cochimi visitors to Loreto of potential agricultural land across the nearby Sierra de la Giganta.
In May 1699 Francisco Maria Piccolo, along with a dozen Cochimí guides and ten Spanish soldiers, crossed the mountains on horseback and entered the valley the Indians called Biaundó, about 20 kilometres (12 mi) inland from the Gulf of California.
Between 1744 and 1758, Miguel del Barco was responsible for building what has been called "the jewel of the Baja California mission churches.
"[3] The Cochimí were nomadic and semi-nomadic hunter-gatherers who dwelt in the austere deserts and mountains of the central portion of the Baja California peninsula.
[7] Several introduced plant species continue to exist or to be grown at the mission: date palms, grapes, citrus, and, notably, ancient olive trees.