By the early 20th century it had fallen into ruins and it was significantly restored under the direction of Leopoldo Torres Balbás in the 1920s.

[6] When Queen Isabella died in November 1504, per her last wishes, she was buried in the convent, inside a 14th-century chamber which was preserved from the former palace.

[7][9]: 168 Two years later, Charles V granted the family of the Counts of Tendilla, descendants of Iñigo López de Mendoza y Quiñones and appointed governors of the Alhambra, the right to be buried in the convent.

[6] By 1703, the convent was again in need of repairs and in 1708 the church was in danger of collapse due to a string of winter storms, which incited authorities to free up funds to address the problems.

They caused significant damage, stripped the palace of its wooden furnishings to use them as fuel for fire, and exacerbated the Alhambra's overall state of neglect.

A partially-preserved poem inscribed along the windows refers to this chamber as a bahw (Arabic: بهو), a word equivalent to the Spanish term mirador (meaning a lookout point), which went on to be a hallmark of Nasrid architecture.

Archeological excavations have discovered remains of carved stucco and tilework, indicating that the hammam was once richly decorated.

[6] The upper walls and the barrel-vaulted roof of the church, missing today, fell into ruin at the end of the 19th century.

The church's former interior has thus been left open to the sky since then, as Torres Balbás stated that there was little point in trying to rebuild them during restoration works.

[6] The original floor of the church was likely lower than it is today and the choir, now disappeared, was connected with the upper level of the cloister next door.

[6] During the restoration works by Torres Balbás in the 1920s, an underground crypt with human remains was discovered beneath the church.

[6] On the west side of the church is the cloister which in its current form is roughly contemporary with the 18th-century tower, according to Torres Balbás.