His two-story villa, built on the south side of the monastic church, consisted of four rooms on each floor. A ramp provided him with easy access to the upper floor where he usually lived. This led to a shady terrace from where he could enjoy a view of the gardens and pools. Inside, the square rooms opened off a central corridor. From the Audience Room a door led to his personal study. Opposite that was his bedroom, which had a specially constructed opening to enable Charles to look down on the altar in the church. Above the altar was hung Titian’s ‘La Gloria’ (sometimes known as 'The Trinity' or 'The Final Judgement' or 'Paradise'), commissioned by Charles in 1550 and completed in 1554. In it Charles is portrayed with his family at prayer, dressed in shrouds, with his crown at his feet, representing his withdrawal from earthly power.
Although he wished for a quieter life he was not completely out of touch with the world that he had once dominated. His sisters, Eleanor and Mary, lived in nearby Jarandilla. Charles asked that his natural son, Jeromin (later known as Don John of Austria) be brought to the village of Cuacos and introduced to him. Other visitors came with news and provided the chance to talk about old times. He communicated regularly with his son Philip and received news and requests for advice brought by couriers from the Low Countries. He was always ready to give voice to his concerns when he heard of instances of Lutheranism in his former lands.
Charles developed a daily routine, adjusted in accordance with the season and his health. Breakfast, prayers with his confessor, time spent with his clocks and, after dressing, mass in the church, would take up his mornings. This would be followed by dinner at midday. He always enjoyed his food. Many of his remaining staff were cooks and regular deliveries enabled them to produce roasted wild boar and venison, black hares marinated in wine, bay leaves and onions, and all kinds of fish. After dinner he would frequently read from his small library - mainly theology, history, philosophy and astronomy - before a siesta. Later in the afternoon he fished in the ponds, visited his aviary, talked to visitors, or discussed theological and philosophical points from sermons or bible readings, sitting on his first floor veranda or in the garden with its terraces and ornamental flower beds, which he continued to re-design. He would usually take a light meal before he retired for the night.
It was in his bed, looking through to the church altar, at about 2-30 a.m. on 21st September 1558, that Charles died, surrounded by monks, his confessor and the Archbishop of Toledo.