The accidental unearthing revealed a large wall of the Buen Suceso hospital, which was thought to be demolished in 1854 along with the Buen Suceso church next door.
While Apple originally considered installing a glass floor in the Madrid store so that visitors could look at the ruins, the plan was abandoned due to the wall's somewhat uninteresting nature.
Instead, Apple plans to "symbolically trace the outline" of the wall in its flooring.
Apple's Madrid store will be span 6,000 square meters and will be tech giant's fourth Madrid location.