After the conquest of the Kingdom of Granada in 1492, he took part in 1501 in crushing the moriscos revolt in the Sierra de los Filabres, province of Almeria conquering the village of Velefique.
Law suits were brought against the inter - racial hate seeking preaches by Lucero, who himself was put in prison and investigated by the new General Inquisitor and Cardinal Francisco Jiménez de Cisneros.
Diego also lost his assignment as a Governor in Oran and Mazalquivir, and some of the castles belonging to the "Fernández de Córdoba" main Aguilar line, were destroyed, for his part in the rebellion.
After the successful conclusion of this military campaign, Diego was awarded the title of Marquis de Comares in 1512 and he became the first Viceroy of Navarre.
His, only son was Luis Fernández de Córdoba y Pacheco, 2nd Marquis of Comares (1482–1564), who succeeded him as Governor of Oran.