Mission founder Father Altimira built a wooden church that was dedicated in 1824. Other missions did not contribute much to the new church, but the Russians at Fort Ross donated some articles, including a Russian-made bell.
After Father Fortuni arrived in 1826, new buildings were built, made of adobe with tile roofs. The church was started in 1827 and finished in 1832. By 1833, the mission's thirty buildings included a 27-room convento, a wooden storehouse, workshops, living quarters for Indian girls, houses for Indian and military families, a gristmill, a jail and an infirmary.
After secularization, settlers in the new town of Sonoma started taking the roof tiles and building materials to build their homes and businesses, and the adobe structures began to crumble. By 1839, the mission was in ruins.
The Historic Landmarks League bought the mission property in 1903, and they finished restoring the mission in 1926, when they turned it over to the State of California. Today, it is part of the Sonoma State Historic Park.