On October 3, the day preceding the festival of St.Francis, bunting and flags from the ships were brought to decorate the new buildings; but, owing to the absence of Moraga, the formal dedication did not take place until October 9.

Happy was Serra's friend and brother, Palou, to celebrate high mass at this dedication of the church named after the great founder of his Order, and none the less so were his assistants, Fathers Cambon, Nocedal, and Pena.
Just before the founding of the Mission of San Francisco, the Spanish Fathers witnessed an Indian battle.

Natives advanced from the region of San Mateo and vigorously attacked the San Francisco Indians, burning their houses and compelling them to flee on their tule rafts to the islands and the opposite shores of the bay.

Months elapsed before these defeated Indians returned, to afford the Fathers at San Francisco an opportunity to work for the salvation of their souls.
In October of the following year, Serra paid his first visit to San Francisco, and said mass on the titular saint's day.

Then, standing near the Golden Gate, he exclaimed: "Thanks be to God that now our father, St.Francis, with the holy professional cross of Missions, has reached the last limit of the Californian continent.