The building also served as a barracks for artillery units and it was attacked and looted by the French when they suppressed the Dos de Mayo Uprising of 1808.

The new premises offered much more space, although the site was not without controversy because of its associations with the Siege of the Alcázar, an episode in the Spanish Civil War, when the castle was held by Nationalist forces.

The new building houses the administrative offices, the Temporary Exhibitions room, the Army room in the present time, the didactic classroom, the auditorium, the archive, the library, the coffee shop, the restoration workshops and the warehouses, all of them endowed with the greatest technical advances for the conservation, restoration, cataloging, investigation and diffusion of the funds that are guarded.

The displays include finds from excavations at the Alcázar which were undertaken prior to construction of the museum extension.

In 1937, the British cryptographer Dilly Knox broke Franco's Enigma, but knowledge of this breakthrough was not shared with the Republicans.