Governor Manuel Micheltorena arrived at San Diego from Mexico in August 1842 with the directive to return the Missions to the management of the Franciscans.
The first Bishop of Alta California Francisco Garcia Diego, OFM, directed Frs. José Jimeno and Juan Moreno to contact Micheltorena for permission to build a seminary in the remains of the quadrangle of Mission Santa Inés. Micheltorena not only gave permission, he also donated 35,000 acres and established an annual annuity of $500 for its maintenance.
In the Seminary's constitution, there is a provision for the education of the young men of the landowners. The wealthy landowners would pay tuition and enough money was set aside for the less fortunate. In 1844 the College of Our Lady de Refugio was erected.
Micheltorena's rule ended abruptly in 1845 when the local landowners who had been evicted successfully lobbied the governor in Monterey, Pio Pico for the return of the Mission lands. Pico then illegally rented them out. The seminary for Franciscans was relocated 1.5 miles east of the Mission in 1846 and there it continued until 1850. In 1852, under the direction of Rt. Rev. José Sadoc Alemany, O.P., Bishop of Monterey, the seminary was re-commissioned to serve as a diocesan college and seminary and re-named Our Lady of Guadalupe. It was also known as College Ranch and provided education for the sons of local ranchers.