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. Many of the whites joined in with Alvarado and Castro, and the affair ultimated in the forced exile of the governor; Castro took his place until Alvarado was elected by the diputacion.
The regular statistics of San Juan cease in 1832, when there were 916 Indians registered. In 1835, according to the decree of secularization, 63 Indians were “emancipated.” Possibly these were the heads of families. Among these were to be distributed land valued at $5120, live-stock, including 41 horses, $1782, implements, effects, etc., $1467.
The summary of statistics from the founding of the Mission in 1797 to 1834 shows 4100 baptisms, 1028 marriages, 3027 deaths. The largest number of cattle owned was 11,000 in 1820, 1598 horses in 1806, 13,000 sheep in 1816.
In 1845, when Pico’s decree was issued, San Juan was considered a pueblo, and orders given for the sale of all property except a curate’s house, the church, and a court-house. The inventory gave a value of $8000. The population was now about 150, half of whom were whites and the other half Indians.
It will be remembered that it was at San Juan that Castro organized his forces to repel what he considered the invasion of Fremont in 1846. From Gavilan heights, near by, the explorer looked down and saw the warlike preparations directed against him, and from there wrote his declaration: “I am making myself as strong as possible, in the intention that if we are unjustly attacked we will fight to extremity and refuse quarter, trusting to our country to avenge our death.”
In 1846 Pico sold all that remained of San Juan Bautista—the orchard—to O. Deleisseques for a debt, and though he did not obtain possession at the time, the United States courts finally confirmed his claim. This was the last act in the history of the once prosperous Mission.