Don Jose de la Guerra was the sponsor, and Captain Font and Surgeon Morelos assisted.
In June, 1809, the image of San Juan was placed on the high altar in the sacristy, which served for purposes of worship until the completion of the church.
By the end of the decade the population had grown to 702, though the number of deaths was large, and it continued slowly to increase until in 1823 it reached its greatest population with 1248 souls.
The new church was completed and dedicated on June 23, 1812.

In 1818 a new altar was completed, and a painter named Chavez demanded six reals a day for decorating.

As the Mission could not afford this, a Yankee, known as Felipe Santiago--properly Thomas Doak--undertook the work, aided by the neophytes.

In 1815 one of the ministers was Esteban Tapis, who afterwards became the presidente.
In 1836 San Juan was the scene of the preparations for hostility begun by Jose Castro and Alvarado against Governor Gutierrez.

Meetings were held at which excited speeches were made advocating revolutionary methods, and the fife and drum were soon heard by the peaceful inhabitants of the old Mission.