During the night the Indians endeavored to escape, one by one, but most of them were killed by the watchful guards.

The next day nothing but the dead and three living women were found.

There were some accusations, later, that Vallejo summarily executed some captives; but he denied it, and claimed that the only justification for any such charge arose from the fact that one man and one woman had been killed, the latter wrongfully by a soldier, whom he advised be punished.
Up to the time of secularization, the Mission continued to be one of the most prosperous.

Jesus Vallejo was the administrator for secularization, and in 1837 he and Padre Gonzalez Rubio made an inventory which gave a total of over $155,000, when all debts were paid.
Even now for awhile it seemed to prosper, and not until 1840 did the decline set in.
In accordance with Micheltorena's decree of March 29, 1843, San Jose was restored to the temporal control of the padres, who entered with good-will and zest into the labor of saving what they could out of the wreck.

Under Pico's decree of 1845 the Mission was inventoried, but the document cannot now be found, nor a copy of it.