The final secularization took place in November, 1834, with Captain Portilla as comisionado and Pio Pico as majordomo and administrator until 1840. There was trouble in apportioning the lands among the Indians, for Portilla called for fifteen or twenty men to aid him in quelling disturbances; and at Pala the majordomo was knocked down and left for dead by an Indian. The inventory showed property (including the church, valued at $30,000) worth $203,707, with debts of $93,000. The six ranches were included as worth $40,437, the three most valuable being Pala, Santa Margarita, and San Jacinto.
Micheltorena's decree of 1843 restored San Luis Rey to priestly control, but by that time its spoliation was nearly complete. Padre Zalvidea was in his dotage, and the four hundred Indians had scarcely anything left to them. Two years later the majordomo, appointed by Zalvidea to act for him, turned over the property to his successor, and the inventory shows the frightful wreckage. Of all the vast herds and flocks, only 279 horses, 20 mules, 61 asses, 196 cattle, 27 yoke oxen, 700 sheep, and a few valueless implements remained. All the ranches had passed into private ownership.
May 18, 1846, all that remained of the former king of Missions was sold by Pio Pico to Cot and José Pico for $2437. Frémont dispossessed their agent and they failed to gain repossession, the courts deciding that Pico had no right to sell. In 1847 the celebrated Mormon battalion, which Parkman so vividly describes in his Oregon Trail, were stationed at San Luis Rey for two months, and later on, a re-enlisted company was sent to take charge of it for a short time. On their departure Captain Hunter, as sub-Indian agent, took charge and found a large number of Indians, amenable to discipline and good workers.
The general statistics from the founding in 1798 to 1834 show 5591 baptisms, 1425 marriages, 2859 deaths. In 1832 there were 27,500 cattle, 2226 horses in 1828, 345 mules in the same year, 28,913 sheep in 1828, and 1300 goats in 1832.