The building that stands today was reconstructed by the Catholic Monarchs. It includes a convent, church and the Santo Domingo cave, where the saint withdrew for penance.

The most notable feature is the church doorway in Gothic Hispanic-Flemish style. It was personally commissioned by Queen Isabella, whose figure sculpted in wood appears praying together with her husband. The church has a single nave with ogive vaulted ceiling. The chapel-cave of Santo Domingo also has a roof with ogive vaults and a beautiful richly decorated doorway. It is currently the headquarters of the Instituto de Empresa.