In 1571, Tomás together with his brother, the future Saint, Francisco de Borja and the Cardinal Alejandrino set out on a trip around Europe that was bound for Rome. Upon arrival in Rome, Tomás was designated the Consultor de la Inquisición Romana, a title affiliated to the Inquisition. Upon returning to Spain, he was appointed cannon of Toledo and Abbot of the Iglesia de la Santísima Trinidad Orense.
In 1599, Philip III of Spain appointed Tomás as the Bishop of Málaga. His ascendancy coincided with an outbreak of pestilence whose origins came from Spanish troops returning from Spanish Morocco and other African conquests. So strong was this plague that people would fall down in the streets and there was nothing that could be medically done to save them, overflowing the capacity of the hospitals. Tomás devoted himself to caring for the sick, even those that nobody would approach due to fear of infection. The plague lasted two years and killed such a large portion of the population that people were brought in from other regions of Spain to fill all the vacant jobs left behind by the dead.
