The transept courtyard is located to the west of La Monteria's courtyard. It was constructed in the 12th century, during the Almohad period, but was later reformed. Ribbed vaults were added during the reign of Alfonso X. The garden had two levels, the highest of which corresponded to the current courtyard, with two main cross-shaped galleries and four peripheral ones, and a second level, 4.7 m below the first, occupied by an orange tree garden divided into four sections, with a large fountain in the centre and pools at the ends.

This lower garden was covered up and filled in with earth after the Lisbon earthquake to form the current rectangular courtyard. The visible remains of this lower floor can be seen from the Crucero courtyard, and the only part that remains are the so-called Mara Padilla baths, which can be accessed from the Danza garden. This basement is made up of a large nave with ten bays that are covered by ribbed vaults. A long barrel vault protects the entrance from the garden.

Today, it is a rectangular courtyard with a garden divided into four quadrants by myrtle hedges, with bonetrees, Jupiter trees, palm trees, bougainvillaea, and jasmine growing within the quadrants.

Several works were completed in the Crucero courtyard and the Gothic palace in the 18th century. The Gothic palace's façade facing the Crucero courtyard was completely renovated in the Baroque style. The courtyard's other façades were also renovated, and the entire garden was buried to raise its floor to the level of the halls. The courtyard corridors' sides were walled off and left as underground chambers.