Moving quickly, on February 10,1851, Bishop Alemany met with John Nobili, S.J. in San Francisco offering Mission Santa Clara to the Jesuits, and the next day sent a letter to Michael Accolti, S.J., who had returned to the Jesuit headquarters in Oregon, inviting the Jesuit Fathers to come to Santa Clara for the purpose of opening a school. As Gerald McKevitt, S.J. states in his 1979 book "The University of Santa Clara," Alemany wrote:

. . . The Mission of Santa Clara will soon be vacant, and might be transferred to you Society for that purpose. It is true that Mission has been squandered, but from all my researches upon the subject of Missions, I entertain the hope that the American Government will feel disposed to give us considerable [property]. At any rate the people of California commence to feel the necessity of education, and could no doubt aid greatly the enterprise.

The invitation was accepted. On March 4, 1851, Alemany sent a message to John Nobili formally appointing him permanent pastor of Santa Clara and administrator of "all belonging to [the] mission." With the transfer taking place officially on March 19, 1851, Father Real left California returning to Mexico, and in May, John Nobili, S.J., as its first president, opened the doors of the College of Santa Clara to a dozen students.

The Mission's adobe buildings were in sad condition with most of the surrounding land being occupied with squatters, whose white tents and frame structures constituted the young village of Santa Clara.

In fact, James Alexander Forbes and his family, who refused to move, occupied part of the mission quadrangle itself. However, after resorting to "novel means" Father Nobili acquired the land and its buildings for the new college. With a starting capital of one hundred and fifty dollars, two teachers and a Hawaiian cook, there were many difficulties in converting the mission into an educational institution. Established in an adobe building on the mission grounds, students were seated on tree trunks and benches in the garden, and at the time of the College's establishment it was not considered safe to venture on foot more than a few yards away from the mission buildings because of half-wild horses, steers and other animals.

(That young institution was to quickly grow as shown by a letter Bernard Reid, a member of the faculty in 1851-52, who wrote that " including day scholars and students who did not attend the examination ceremonies, there were about 60 young men at Santa Clara in 1851-52; although it would be a long time before expenses stopped being in excess of the income derived from the pupils.)