The original church was founded in 1460 and was located on the banks of the Manzanares River.  I was later moved to its current location due to a monk's insistence to Queen Isabel La Católica of the unsanitary conditions of living close to the river. The monastery was built again stone by stone carried by the same monks to the new site.

The monastery had two cloisters, of which there is now only one, restored inside Moneo's new cube.

The monastery is was the location for all swearing-in ceremonies of Spanish princes from Philip II to Isabel II. 

Napoleon´s troops occupied the monastery during the French invasion, using it as its artillery park and destroying both cloisters and the Gothic facade. 

The church was designed with just one central nave and two chapels on the sides, a transept, apse and the choir at its base. The Gothic vault is the only part thatremains original.