There were seven hundred and forty neophytes at that time under missionary care, though Lasuen spoke most disparagingly of the location as a Mission site.
In 1824 San Diego registered its largest population, being then eighteen hundred and twenty-nine.
When Spanish rule ended, and the Mexican empire and republic sent its first governor, Echeandia, he decided to make San Diego his home; so for the period of his governorship, though he doubtless lived at or near the presidio, the Mission saw more or less of him.

As is shown in the chapter on Secularization, he was engaged in a thankless task when he sought to change the Mission system, and there was no love lost between the governor's house and the Mission.
In 1833 Governor Figueroa visited San Diego Mission in person, in order to exhort the neophytes to seize the advantages of citizenship which the new secularization regulations were to give to them; but, though they heard him patiently, and there and at San Luis Rey one hundred and sixty families were found to be duly qualified for "freedom," only ten could be found to accept it.
On March 29, 1843, Governor Micheltorena issued a decree which restored San Diego Mission temporalities to the management of the padre.

He explained in his prelude that the decree was owing to the fact that the Mission establishments had been reduced to the mere space occupied by the buildings and orchards, that the padres had no support but that of charity, etc.

Mofras gives the number of Indians in 1842 as five hundred, but an official report of 1844 gives only one hundred.

The Mission retained the ranches of Santa Isabel and El Cajon until 1844-1845, and then, doubtless, they were sold or rented in accordance with the plans of Pio Pico.
To-day nothing but the _fachada_ of the church remains, and that has recently been braced or it would have fallen.