This museum, which is considered by some to be the most interesting Byzantine Church in Istanbul due to its magnificent mosaics and frecoes, was originally built in the late 11th century by Maria Doukaina , the mother in law of Emperor Alexius I Commenus, on the remains of and earlier Byzantine church.

It was converted into a mosque in 1511 by the Grand Vezir Atik Ali Pacha during the reign of Sultan Beyazid II, and the mosaics were subsequently plastered over.

In the 1948 the mosque was turned into a museum and between the years 1947-1952, a team of American restoration experts uncovered the valuable mosaics which had been for centuries covered with plaster. These mosaics are amonth the greatest examples of Byzantine art in existence today.