Later he entered in the convent of San Pablo de Córdoba and became professor of arts and theology where he gained the reputation as a prolific scholar.

Cristóbal Vaca de Castro, who was sent by the Spanish crown to impose order on the newly conquered territories, asked Fray Tomás to establish a provisional government in Peru.

It is said that he was selected by Vaca de Castro for the task because of his moral authority and the prestige he enjoyed.

On June 27, 1552, he was appointed by Pope Julius III as Bishop of La Plata o Charcas.

[2] After his work as priest and scholar over 25 years, he was appointed the first rector magnificus of National University of San Marcos.