The mission was founded by the Franciscan order on October 9, 1791, to convert the Native Americans living in the area to Catholicism.

Spanish Governor José Joaquín de Arrillaga was buried in the chapel after he died on July 24, 1814, during a visit to the Mission.

In 1954, when the Mission Soledad restoration was begun, only piles of adobe dirt and a few wall sections from the cuadrángulo (quadrangle) remained.

The chapel was reconstructed and dedicated under the auspices of the Native Daughters of the Golden West on October 9, 1955.

The Mission Nuestra Señora de la Soledad is now a functioning Catholic chapel and public museum.