In 1587 Philip II honoured his Desire to return to his native Spain, naming him chaplain to his sister, the Dowager Empress María, daughter of Charles V, who had been living in retirement with her daughter Princess Margarita at the Monasterio de las Descalzas de S Clara at Madrid from 1581. In 1591, Victoria became a godfather to his brother Juan Luis's daughter, Isabel de Victoria. Victoria worked for 24 years at Descalzas Reales, serving for 17 years as chaplain to the Empress until her death, and then as convent organist. Victoria was also being paid much more at the Descalzas Reales than he would have earned as a cathedral chapelmaster, receiving an annual income from absentee benefices from 1587–1611. When the Empress Maria died in 1603, she willed three chaplaincies in the convent, with one going to Victoria. According to Victoria, he never accepted any extra pay for being a chapelmaster, and became the organist rather than the chapelmaster. Such was the esteem in which he was held that his contract allowed him frequent travel away from the convent. He was able to visit Rome in 1593 for two years, attending Palestrina's funeral in 1594. He died in 1611 in the chaplain's residence and was buried at the convent, although his tomb has yet to be identified.