The last and northernmost California mission, Mission San Francisco Solano was the only mission founded after Mexico's independence from Spain. It was also the only mission founded without the prior approval of the Church.

The brash Father Jose Altimira, sent from Spain in 1819 to assist at Mission Dolores, devised a plan to found a new mission to the north where the climate was warmer. Instead of going to his proper church superiors he made his proposal to Governor Don Luis Arguello, who was responsible for keeping the Russians out of Northern California. Father Altimira's plan to move both the Dolores and the San Rafael missions to Solano seemed to be the solution to the Governor's concern about the Russian encroachment in his province.

Eventually the Church gave their approval for the new Mission San Francisco Solano, to be run by Father Altimira, but insisted that Missions Dolores and San Rafael is left undisturbed.

The new mission seemed to get off to a good start. The vineyards were flourishing. But soon the cruelty of Father Altimira became evident. His constant flogging and imprisonment of the Native Americans, in his efforts to "civilize" them soon caused a revolt. A large group of angry Native Americans attacked the mission in 1826. After looting and burning buildings and supplies, they forced Father Altimira to flee to Mission San Rafael. Soon after that, unwelcome at any of the missions, he returned to Spain.

His replacement was the faithful and kind Father Fortuni. After spending several years rebuilding the mission he restored it to its former strength. His new adobe buildings had tile roofs, and a convento with 27 rooms made up a large part of the quadrangle.

Barely finished, the mission was secularized in 1834 and came under the control of General Mariano Vallejo. He was supposed to see that the mission properties were distributed to the Native Americans. Instead he claimed the mission property to be his own and added it to his already vast property holdings in the area. With the promise of protection, room and board, he put the Native Americans to work for him.

Vallejo built up a large pueblo town in Sonoma, and for a while maintained the mission church. Eventually, the settlers removed the roof tiles and timbers for use in their own buildings and the mission's adobe walls began to dissolve. A new adobe church was built for the parish at the same site of the original mission church.

When the Americans arrived in Sonoma to take control of California from Mexico, General Vallejo was imprisoned. For a brief time the Mission Solano continued to serve as a parish church for the new American settlement.

The Historic Landmarks League purchased the mission property in 1903, and with state funds, restored the Mission Solano. When complete, in 1926, the League turned the property over to the state. Further restoration was then done and the mission is now the Sonoma Mission State Historic Park.