In 1823, Spaniard José Altimira established Mission San Francisco Solano, under the direction of Governor Luis Antonio Argüello.

The mission, the only to be constructed not by the Spanish but by the later Mexican authorities seeking independence and succeeding to the Royal Spanish Viceroyalty at that time, was built as part of a larger plan Governor Luis Antonio Argüello had devised to fortify the Spanish presence north of the San Francisco Bay and thus deter Russian Empire (Russia) encroachment southward from further north in Russian America (where they'd established a presence back in the 1740s, a half-century before) into the Pacific Ocean coastal region.

[16] Franciscan padre / priest José Altimira worked with Governor Argüello to plan the mission, against the desires of José Francisco de Paula Señan, then the President-General of the Spanish missions in California, who disapproved of secular government intervention into religious matters.

A decade later in 1833 the Congress of the Union (Mexican Congress) passed the Mexican secularization act of 1833, ending Roman Catholic Church mission stewardship and control of huge tracts of associated lands in California, one goal being to diminish the church's highly influential standing in California's economy and political system.

[18] Governor Figueroa had received instructions from the Mexican Congress further south in the capital city of Mexico City to establish a strong presence in the region north of the San Francisco Bay to protect the area from encroachments of foreigners.

[19] An immediate concern was the further south and eastward movement to the interior of the Russian America Company from their settlements at Fort Ross and Bodega Bay on the Northern California coastline.

[20] Figueroa's next step in implementing his instructions was to name Lieutenant Vallejo as Military Commander of the Northern Frontier and to order the Army units of officers / soldiers, arms and materiel supplies at the Presidio of San Francisco moved to the site of the recently secularized Mission San Francisco Solano.

[21] In 1834, George C. Yount, the first European American permanent settler in the Napa Valley, north of San Francisco Bay, was employed as a carpenter by Mexican Army General Vallejo.

The Governor granted Lieutenant Vallejo the initial lands (approximately 44,000 acres (178 km2)) of Rancho Petaluma immediately west of Sonoma.

Vallejo was also named Director of Colonization which meant that he could initiate land grants for other colonists (subject to the approval of the governor) and the diputación (Alta California's nominal assembly / legislature).

In 1835, with the assistance of William A. Richardson, he laid out a grid, in accordance with the Spanish Laws of the Indies, of the streets, building lots, central plaza and broad main avenue of the newly planned Pueblo de Sonoma.

In 1843, now Lieutenant Colonel Vallejo wrote to the Governor recommending that a civil government be organized for Sonoma.

[24] Before dawn on Sunday, June 14, 1846, thirty-three Americans, already in rebellion against the Alta California provincial government of Mexico, arrived in Sonoma.

Some of the group had traveled from the camp of United States Army Brevet Captain John C. Frémont (1813-1890), who had entered California illegally from across the Great Plains and through the Rocky Mountains chain from the east in late 1845 with his exploration and mapping expedition.

As the number of immigrants arriving in California had swelled, the Mexican government barred them from buying or renting land and threatened them with expulsion because they had entered without official permission.

[25][26] Mexican officials were concerned about the coming Mexican–American War of 1846-1848, with the United States coupled with the growing influx of American and other European immigrants into California, both by overland wagon trains from the east and by ship on the West Coast and Pacific Ocean.

[27] A group of rebellious Americans had departed from Captain Frémont's military camp on June 10 and captured a herd of 170 Mexican government-owned horses being moved by Californio / Mexican Army soldiers from San Rafael and Sonoma to Alta California's Commandante General José Castro in Santa Clara.

William Ide (1796-1852), gave an impassioned speech urging the rebels to stay in Sonoma and start a new republic.

[32] The Sonoma Barracks became the headquarters for the remaining twenty-four rebels, who within a few days created their Bear Flag.

[37] When the California interim government and U.S. military occupation beginning 1846, finally ended after four years in 1850, when California was admitted as the 31st state to the federal Union by act of the U.S. Congress]], approved by the President, on September 9, 1850, Sonoma was then named the first county seat town for Sonoma County.

[38] Surrounding towns such as Petaluma and Santa Rosa were developing and gaining population much faster than Sonoma.

An 1854 special election then moved the county seat and courthouse and its legal work and entailed economic activity to Santa Rosa.

[39] The United States Navy operated a rest center at the Mission Inn through World War II.

[40] Parts of Wes Craven's Scream (1996) were filmed in the city, with shots of the Sonoma Community Center masked as Westboro High School.

The active Rodgers Fault lies to the west of Sonoma Creek; however, the risk of major damage is mitigated by the fact that most of the soils beneath the city consist of a slight alluvial terrace underlain by strongly cemented sedimentary and volcanic rock.

[42] To the immediate south, west and east are deeper rich, alluvial soils that support valuable agricultural cultivation.

Apple's desktop operating system, macOS Sonoma, announced on June 5, 2023, during WWDC, is named after the city.