Ceinos was also president of the audiencias that served as interim governments of New Spain from 1564 to 1566 and from approximately July 1568 to November of that year.
Ceinos served a third term in 1568, from July to November, when the Audiencia took charge pending the arrival of new Viceroy Martín Enríquez de Almanza.
At this time the Audiencia included (besides Ceinos), Pedro Villalobos, Jerónimo Orozco and Vasco de Puga.
He strongly opposed the exploitation of the Indigenous through the institutions of slavery, the encomienda system, forced labor and tribute.
In this report he wrote of the decimation of the Indigenous resulting from the Spanish conquest: It is certain that from the day that Don Hernando Cortés, Marques del Valle, entered this land, in the seven years, more or less, that he governed, the natives suffered many deaths, much maltreatment, robbery and violence, taking advantage of their labor and their lands, without order or moderation.... A large part of the population disappeared, as much from the excessive tribute and maltreatment as from the diseases and smallpox, so that in this time the population is considerably less, especially in the hot lands.