But orders soon began to come in for the delivery of cattle and horses, applications rapidly came in for grants of the Mission ranches, and about the middle of June, 1841, the lands were divided among the ex-neophytes, about 100 in number, and some forty whites.

At the end of July regulations were published for the foundation of the pueblo, and Don Juan Bandini soon thereafter went to supervise the work.

He remained until March, 1842, in charge of the community property, and then left about half a dozen white families and twenty or more ex-neophytes duly organized as a pueblo.
In 1843 San Juan was one of the Missions the temporalities of which were to be restored to the Padres, provided they paid one-eighth of all produce into the public treasury.

In 1844 it was reported that San Juan had no minister, and all its neophytes were scattered.

In 1845 Pico's decree was published, stating that it was to be considered a pueblo; the church, curate's house and court-house should be reserved, and the rest of the property sold at auction for the payment of debts and the support of public worship.