The two prominent domes, set one behind the other, represent an attempt at a design feature reminiscent of St. Irene of Constantinople and the St. John's Basilica at Ephesus. Awkwardly juxtaposed above the three remaining domes, the larger two create a prayer hall that was to become a theme in the architecture of Ottoman mosques.

The mosque forms a part of the külliye, or complex, comprising a medrese, a hamam, a hospital, and the tomb of the Sultan Beyazit I, built by his son Süleyman the Magnificent in 1406.