The Spanish divided California into two parts, Baja California and Alta California, as provinces of New Spain (Mexico). Baja or lower California consisted of the Baja Peninsula and terminated roughly at San Diego, California, where Alta California started. The eastern and northern boundaries of Alta California were very indefinite, as the Spanish, despite a lack of physical presence and settlements, claimed essentially everything in what is now the western United States.

The first permanent mission in Baja California, Misión de Nuestra Señora de Loreto Conchó, was founded on October 15, 1697, by Jesuit priest Juan Maria Salvatierra (1648–1717) accompanied by one small boat's crew and six soldiers. After the establishment of Missions in Alta California after 1769, the Spanish treated Baja California and Alta California, known as Las Californias, as a single administrative unit with Monterey as its capital, and falling under the jurisdiction of the Viceroyalty of New Spain based in Mexico City.

Nearly all the missions in Baja California were established by members of the Jesuit order supported by a few soldiers. After a power dispute between Charles III of Spain and the Jesuits, the Jesuit colleges were closed and the Jesuits were expelled from Mexico and South America in 1767 and deported back to Spain. After the forcible expulsion of the Jesuit order, most of the missions were taken over by Franciscan and later Dominican friars. Both of these groups were under much more direct control of the Spanish monarchy. This reorganization left many missions abandoned in Sonora Mexico and Baja California. Concerns about the intrusions of British and Russian merchants into Spain's colonies in California prompted the extension of Franciscan missions to Alta California, as well as presidios.