The California Governor wanted a robust Mexican presence north of the San Francisco Bay to keep the Russians who had established Fort Ross on the Pacific coast from moving further inland.

A young Franciscan friar from Mission San Francisco de Asis wanted to move to a location with a better climate and access to a larger number of potential converts.

José Altimira at age 33 arrived from Barcelona, Spain, to serve at Mission San Francisco de Asís.

California Governor Luis Argüello was interested in blocking the Russians at Bodega Bay and Fort Ross from moving further inland.

[10] Under the old Spanish regime, founding a new mission required the approval of both New Spain's Bishop and the King's Viceroy.

Altimira, with military escorts, began exploring north of the Bay for a suitable mission site.

[14][15] A detachment of soldiers from the Presidio of San Francisco would be provided to protect the Mission and guard the neophytes.

[16] Altimira with soldiers and neophytes primarily from Mission San Francisco de Asís returned to the Sonoma area near the end of August.

His annual report for 1823 listed no baptisms, one marriage, one funeral, a population of 482 Indians (all transferred from other missions) and 1341 animals.

Indians not living at the Mission were unhappy with the amount allocated for their work; they burned some of the wooden buildings in protest.

Buenaventura Fortuni, an aging Spanish Franciscan who had been working at Mission San José in California, was assigned to replace Altimira.

Completing this enclosure were workshops where the Indians were taught to be craftsmen and created the items needed to help the mission be self-sufficient.

In addition to the quadrangle, there were orchards, gardens, vineyards, fields of grain, a gristmill, houses for the soldiers and Indian families, a jail, a cemetery, and an infirmary.

Gutierrez recorded the following: 127 baptisms, 34 marriages, and 70 deaths; a total of 996 neophytes (coming from 35 area villages[26]); the livestock inventory included 6,000 sheep and goats, 900 horses, 13 mules, 50 pigs and 3,500 head of cattle.

Governor Figueroa issued a regulation (Reglamento Provisional para la secularization de las Misiones) on August 9, 1834, outlining the requirements for the distribution of property (land, cattle, and equipment) to each mission's neophytes.

[29] Mission San Francisco Solano officially ceased to exist on November 3, 1834, when it was designated a First Class Parish.

[30] Lieutenant (teniente) Mariano Vallejo, Commandant of the Presidio of San Francisco, was named administrator (comisionado) to oversee the closing of the Mission under the Reglamento.

Quijas moved back to San Rafael in July 1835, after many disputes with Guadalupe Antonio Ortega, Vallejo's majordomo to whom he had delegated the work of secularization.

[33] Right after returning to San Rafael, Padre Quijas wrote a letter to Commissary Perfect Garcia Diego, his superior, complaining about the situation in Sonoma and specifically the "abominable deeds of Ortega."

Quijas left, the neophyte population decreased rapidly, most returning to their home villages – taking their movable property with them – or moving to ranchos {including Vallejo's Petaluma Adobe} to work, or staying in Sonoma as servants.

)[38] In August 1839, the government sent William Edward Petty Hartnell as Visitador General de Misiones to check compliance with the Reglamento but Vallejo avoided responding – claiming he did not have time because of military affairs.

After the 1940s, the former church and Convento were remodeled along more authentic lines suited to exhibits devoted exclusively to mission history.

[45] European diseases such as measles and smallpox, for which Native Americans had no inherited resistance, together with the overcrowded and unhealthy living conditions (by today's standards) at all California missions (especially for women and children) contributed to the high death rate.

[46] However, the missions served, with the resources of the time, the health needs of its inhabitants, including those of Indian origin.