It is also referred to as the "Palace of the Habsburgs" and is constructed on two stories surrounding the Patio de Mascarones and the presbytery of the Basilica, taking up the full façade of El Escorial (Courtyard of Masks). It uses the same architectural style as the Charles I Palace in the Yuste Monastery. At this time, only the Battle Room and the Royal Quarters can be visited. Important paintings from the early 17th-century Spanish school, the 16th-century Italian and Venetian schools, and the 16th- and 17th-century Flemish schools, notably Saint Christopher at the Ford by Joachim Patinir, may be seen in the Kings' private quarters.

The Ambassadors' Hall, one of the rooms you pass through before entering the royal chambers, has a number of interesting artifacts on display, including 17th-century mortars, an ivory-inlaid table, two floor-mounted sundials, two Chinese folding chairs from the Ming dynasty (circa 1570), and portraits of all the monarchs of the House of Austria. Special attention should be made of the magnificent marquetry doors, a gift from Emperor Maximilian II. The rumored chair-bench that Philip II is thought to have used to make his final trip to the abbey while suffering from gout is also on show.

The soberly adorned chambers that make up the "King's House" are there since that is where the austere Philip II lived. The window of the royal bedroom, which is situated adjacent to the basilica's main altar, permitted the king to attend mass from his bed when his gout prevented him from doing so. The main room, the writing desk, the bedroom, and the lavish oratory are the four rooms that make up this house.