Transition between Church and Mosque
In 1453 Sultan Mehmed laid siege to Constantinople, driven in part by a desire to convert the city to Islam. The Sultan promised his troops three days of unbridled pillage if the city fell, after which he would claim its contents himself. The Hagia Sophia was not exempted from the pillage, becoming its focal point as the invaders believed it to contain the greatest treasures of the city. Shortly after the city’s defenses collapsed, pillagers made their way to the Hagia Sophia and battered down its doors. Throughout the siege the Holy Liturgy and Prayer of the Hours were performed at the Hagia Sophia, and the church formed a refuge for many of those who were unable to contribute to the city’s defense. Trapped in the church, congregants and refugees became booty to be divided amongst the invaders. The building was desecrated and looted, and occupants enslaved or slaughtered; a few of the elderly and infirm were killed, and the remainder chained. Priests purportedly continued to perform Christian rites until stopped by the invaders. When the Sultan and his cohort entered the church, one of the Ulama climbed the pulpit and recited the Shahada, transforming at once the church into a mosque.

Mosque
Immediately after the Ottoman Turks conquered Constantinople in 1453, the Hagia Sophia was converted into the Ayasofya Mosque. As described by several Western visitors (such as the Córdoban nobleman Pero Tafur and the Florentine Cristoforo Buondelmonti), the church was in a dilapidated state, with several of its doors were off; sultan Mehmed II ordered the cleanup of the church and its conversion. The subsequent sultan, Bayezid II, had a new minaret built to replace that errected by his father.

In the 16th century the sultan Suleiman the Magnificent (1520–1566) brought back two colossal candles from his conquest of Hungary. They were placed on both sides of the mihrab. During the reign of Selim II (1566–1577), the building started showing signs of fatigue and was extensively strengthened with the addition of structural supports to its exterior by the great Ottoman architect Mimar Sinan, who is also considered one of the world's first earthquake engineers.[23] In addition to strengthening the historic Byzantine structure, Sinan built the two additional large minarets at the western end of the building, the original sultan's loge, and the mausoleum of Selim II to the southeast of the building (then a mosque) in 1577. The mausoleums of Murad III and Mehmed III were built next to it in the 1600s.

Sultan Mahmud I ordered the restoration of the building in 1739 and added a medrese (a Koranic school, now the library of the museum), a soup kitchen (for distribution to the poor) and a library, and in 1740 a fountain for ritual ablutions (Şadirvan), thus transforming it into a külliye, i.e. a social complex. At the same time a new sultan's gallery and a new mihrab were built inside.

The most famous restoration of the Hagia Sophia was ordered by Sultan Abdülmecid and completed by eight hundred workers between 1847 and 1849, under the supervision of the Swiss-Italian architect brothers Gaspare and Giuseppe Fossati. The brothers consolidated the dome and vaults, straightened the columns, and revised the decoration of the exterior and the interior of the building. The mosaics in the upper gallery were cleaned. The old chandeliers were replaced by new pendant ones. New gigantic circular-framed disks or medallions were hung on columns. They were inscribed with the names of Allah, the Prophet Muhammad, the first four caliphs Abu Bakr, Umar, Uthman and Ali, and the two grandchildren of Mohammed: Hassan and Hussain, by the calligrapher Kazasker İzzed Effendi (1801–1877). In 1850 the architect Fossati built a new sultan's gallery in a Neo-Byzantine style connected to the royal pavilion behind the mosque. Outside the Hagia Sophia, a timekeeper's building and a new madrasah were built. The minarets were altered so that they were of equal height. When the restoration was finished, the mosque was re-opened with ceremonial pomp on 13 July 1849.

Museum, current use
In 1935, the first Turkish President and founder of the Republic of Turkey, Mustafa Kemal Atatürk, transformed the building into a museum. The carpets were removed and the marble floor decorations appeared for the first time in centuries, while the white plaster covering many of the mosaics was painstakingly removed by expert restorers. Turkish fine art photographer Ahmet Ertuğ's close-up pictures of the restored mosaics can be viewed in the upper northern gallery of the Hagia Sophia in a permanent exhibition. The museum's hours are 9.30am to 4.30pm, Tuesday through Sunday; entry fee is 20 TL, or free with the use of a Museum Card.

Use of the complex as a place of worship (mosque or church) is strictly prohibited. However, in 2006, it was reported that the Turkish government allowed the allocation of a small room in the museum complex to be used as a prayer room for Christian and Muslim museum staff.