Almost as bad as warlike Indians were the earthquakes of that year, several in number, which cracked all the adobe walls of the buildings and compelled everybody--friars and Indians--to sleep out of doors for safety.
In 1803 the governor ordered the padres of San Juan to remove their stock from La Brea rancho, which had been granted to Mariano Castro. They refused on the grounds that the rancho properly belonged to the Mission and should not have been granted to Castro, and on appeal the viceroy confirmed their contention.
In June of this year the corner-stone of a new church was laid. Padre Viader conducted the ceremonies, aided by the resident priests. Don José 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 Estéban Tapis, who afterwards became the presidente.
In 1836 San Juan was the scene of the preparations for hostility begun by José 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.