When he arrived in Mexico City, he immediately took steps to end the turmoil left by the former president of the Real Audiencia, Alonso Muñoz.

In 1570 the viceroy personally led an expedition against the Indian tribes that had been devastating the interior, but he did not give into demand for total war against the Chichimeca.

He established hospitals in the city to treat the victims of a terrible epidemic (thought to be chicken pox or varicella) that left 3,000 people dead.

He published regulations in which the social protection of the Indians was guaranteed against their Spanish patrons, and a fair salary was assured for those who worked as peasants and farmers.

Composed of a group of high-ranking bishops and sometimes led by the archbishop of Mexico City, the Inquisition had special instructions to oversee and control the religious practices of Spaniards and non-indigenous residents in the territory, and to eradicate any crypto-Jewish communities (judaizantes), as well as any Protestants.

Most of these 200 people were burnt alive in public plazas or tortured to death in secret dungeons, both scattered throughout what is now downtown Mexico City.

[citation needed] King Philip II of Spain received outstanding comments about this viceroy, and he was aware of the obvious improvements made during his administration.

The Audiencia governed New Spain until the arrival of the next viceroy, Lorenzo Suárez de Mendoza, 5th Count of Coruña.