Alonso de Covarrubias, a Renaissance architect, created the Ducal Palace of Pastrana, a Renaissance structure, in the 16th century. In 1941, it was designated as a national monument, and in 1966, as a historic-artistic site.

The Ducal Palace (created by Antonio Fernández Alba) has a square floor layout with corner towers and a central courtyard. In the back of the palace is a tiered garden. The palace never reached completion for a number of legal reasons.

The palace's façade is made of ashlar masonry and doesn't have many decorations. The main façade, which is in Renaissance style and bears the inscription "De Mendoza y de La Cerda," stands out in the center for its Italianate character. Coffered ceilings in the Plateresque style can be found within, which were also created by Alonso de Covarrubias. The lower portion of the structure is decorated with Toledo-made tiled skirting boards in the Mudejar style and 19th-century Chinese furniture, while the walls are covered with tapestries created by Mudejar artist Luis Cienfuegos.

Its design dates back to 1541, the year that the Princess of Éboli's grandmother, Ana de la Cerda y Castro, bought the village of Pastrana. The Princess of Eboli was imprisoned in her palace in 1581, and there she passed away in 1592 while being cared for by her three servants and youngest daughter, Ana de Silva (who would later become a nun).

The Plaza de la Hora, which gets its name from the princess's ability to leave the palace for an hour each day, is noted for its latticed balcony. After Antonio Pérez's flight to the Kingdom of Aragon in 1590, Philip II ordered the Ducal Palace's doors and windows to be grilled. Mara Ana de Austria, the daughter of Mara de Mendoza and Juan de Austria, was also born there.

The Carlos Clemente and Antonio Fernández Alba-designed palace was purchased by the University of Alcalá in 1997, and it was finished during that year.