In July, 1839, a party called Yozcolos, doubtless after their leader, attacked the neophytes guarding the Santa Clara wheat-fields, killing one of them.  The attackers were pursued, and their leader slain, and the placing of his head on a pole seemed to act as a deterrent of further acts for awhile.

In December of the same year Prado Mesa made an expedition against gentile thieves in the region of the Stanislaus River.  He was surprised by the foe, three of his men killed, and he and six others wounded, besides losing a number of his weapons.  This Indian success caused great alarm, and a regular patrol was organized to operate between San Jose and San Juan Missions for the protection of the ranches.  This uprising of the Indians was almost inevitable.  Deprived of their maintenance at the Missions, they were practically thrown on their own resources, and in many cases this left them a prey to the evil leadership of desperate men of their own class.

Santa Clara was one of the Missions immediately affected by the decree of Micheltorena, of March 29, 1843, requiring that the padres reassume the management of the temporalities.  They set to work to gather up what fragments they could find, but the flocks and herds were “lent” where they could not be recovered, and one flock of 4000 sheep—­the padre says 6000—­were taken by M.J.  Vallejo, “legally, in aid of the government.”

Pio Pico’s decree of June 5, 1845, affected Santa Clara.  Andres Pico made a valuation of the property at $16,173.  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.  Its walls were five feet thick.  The adobe bricks were thrown out upon the plaza behind the cross.

The present occupation of Santa Clara as a university as well as a church necessitated the adaptation of the old cloisters to meet the modern conditions.  Therefore the casual visitor would scarcely notice that the reception-room into which he is ushered is a part of the old cloisters.  The walls are about three feet thick, and are of adobe.  In the garden the beams of the cloister roofs are to be seen.