[6][verification needed] This grant confirms the endowment by Mehmed II of the Greek Orthodox Church of Saint Mary of the Mongols, the only church in Istanbul that was never converted into a mosque, to the mother of Christodoulos (the Bayezid II Mosque's architect's grandmother) in acknowledgment of the two architects' work.

[7] In 19th-century and early 20th-century accounts of the city it is often referred to as "the Pigeon Mosque" because of the large number of birds that congregated nearby to be fed by worshippers.

An elevated sultan's loge (hünkâr mahfili), located to the right of the mihrab, is supported by ten small marble columns which were reused from earlier Byzantine churches.

Originally designed as four domed cells to serve as a hospice for wandering dervishes, the wings were integrated into the prayer hall in the sixteenth century and now consist of three consecutive rooms separated by archways.

Behind the mosque is a small garden, containing the türbe (tombs) of Sultan Bayezid II, his daughter Selçuk Hatun, and Grand Vizier Koca Mustafa Reşid Pasha.

[1] Below the garden is an arcade of shops (arasta), designed by Mimar Sinan in 1580, whose rents were originally intended to support the mosque.

In 1882 the former soup kitchen was converted into the State Library of Istanbul by Sultan Abdulhamid II; it now houses over 120,000 books and 7000 manuscripts.

[citation needed] The former medrese now houses a small Museum of Turkish Calligraphy Art that has been closed to the public for more than a decade.

[15] Embedded in the lowest part of the walls are fragments of sculpture from the lost triumphal arch from the Forum of Theodosius, more remains of which are scattered on the ground across the road from the mosque.