There were then 130 ex-neophytes, the live-stock had dwindled down to 430 cattle, 215 horses, and 809 sheep.

The padre found it necessary to write a sharp letter to the alcalde of San Jose on the grog-shops of that pueblo, which encouraged drinking among his Indians to such extent that they were completely demoralized.
March 19, 1851, the parish priest, who was a cultivated and learned Jesuit, and who had prepared the way, succeeded in having the Santa Clara College established in the old Mission buildings.

On the 28th of April, 1855, it was chartered with all the rights and privileges of a university.

In due time the college grew to large proportions, and it was found imperative either to remove the old Mission structure completely, or renovate it out of all recognition.

This latter was done, so that but little of the old church remains.
In restoring it in 1861-1862 the nave was allowed to remain, but in 1885 it was found necessary to remove it.