The origins of the “official” name for first California mission (San Diego de Alcala) and the reference to this as the “Mother of all Missions” is a little convoluted. San Diego Bay was discovered by Juan Rodriquez Cabrillo in 1542 but given its present name by Captain Sebastian Vizcaino when he explored the coast in 1602. The name was subsequently applied to both the first Spanish presidio (fort) and the first mission in Alta California by Fr. Junipero Serra at the official founding of the mission, on July 16, 1769. Saint Didacus of Alcala (c.1400-1463), the patron saint of the mission, was a Spanish hermit who became a brother in the Franciscan order. He was canonized by the Franciscan Pope Sixtus V in 1588.
The early reports from the Spanish missionaries referred to this mission as San Deigo de Alcala and sometimes included the name of the native village where the mission was established but in later documents San Diego is referred to only as San Diego de Alcala. As far as we know popular or descriptive names for the missions did not began to appear until the early 1900s. Fr. Zephyrin Engelhardt, O.F.M. wrote the definitive early history of the missions (a multi-volume work entitled Missions and Missionaires of California) the first volume of which was published in 1908. Later, Fr. Engelhardt published individual books on each of the missions. His book on the San Diego Mission was published in 1930. As far as we know Fr. Engelhardt is the source of the capsule descriptions now used for many of the missions.
Since San Diego de Alcala was the first mission it was quite logically called “The Mother of All Missions.”
The natives had no role in the naming of the mission or its description as the Mother of All Missions.
I am attaching a photo of Fr. Engelhardt and an early sketch of the San Diego Mission.
Fr. Zephyrin Engelhardt, O.F.M.
San Diego de Alcala c. 1850