In 1536 De Quiroga was appointed the first bishop of the newly established diocese of Michoacán. He was nominated by the President of the Second Audiencia, Bishop of Santo Domingo, Sebastián Ramírez Fuenleal, after the first candidate Fray Luis de Fuensalida had declined the honor. The Emperor and the Pope approved the nomination and in 1537 the appointment was made official; in 1538 he took office. He remained in Michoacán as pastor and protector of the Indians for most of the remainder of his life.