Trabzon Ayasofya Church which serves as a museum today was constructed in the time of Manuel Comnenos I (1238-1263), one of the kings of Trabzon Empire. The bell tower to the west of the church was dated back to 1427 by the British traveller and researcher G. Finlay. On the west of the church are the remains of a chapel with three apses which is supposed to have belonged to an earlier period.

Following the conquest of Trabzon by Sultan Mehmet the Conqueror, the structure was turned into a mosque and declared as a monument of foundations. Ayasofya had always drawn the attention of the travellers and scholars who visited the city for centuries. Among those are Evliya Çelebi (1648), Pitton Tournefort (1701), Hamilton (1836), Texier (1864), Şakir Cevdet from Trabzon (1878) and Lynch (1893). The mosque which was ruined in time was renovated by the efforts Rıza Efendi from Bursa in 1864. During the World War I, the mosque building was used as a store house and a hospital before serving as a mosque again. Between 1958 and 1962, the mosque was restored to a museum with the cooperation of Edinburgh University and Directorate General of Foundations, and it was opened to visitors aſter 1964.

The structure which exemplifies the Byzantine churches of the late period best was constructed with a square and cross shaped plan. Covered with a high central dome, the building has a narthex (hall at the entrance) and three naves. The nave at the centre is pentagonal, and the other two have semicircular apses. On the narthex, there is a chapel.

On the north, west and south sides of the structure are entrances with porticos. Its dome is supported by monolithic four marble columns, and arches and pendentives, and its dome and tambour are twelve cornered. The structure was covered with different vaults around the central dome, and its roof was tiled in a way which gives different altitudes.

Of superior workmanship, stone reliefs of the structure reflect not only the influence of Christian art, but also that of Islamic art. Medallions decorated with interlocking geometric designs on the north and west sides as well as the porticos and niches on the west side bear the characteristics of stone carvings of the Seljuk period.

The most splendid side of the structure is the south. Here on this side, the creation of Adam and Eve is depicted on a basrelief frieze. A single headed eagle motif decorates the keystone of the arch on the south side, being the symbol of the Comnenos who ruled the city for 257 years. Exterior of the main apse on the eastern side is a similar eagle depiction. Again on this side are the figures of mythological characters such as centaurs and griffons, pigeon motifs, square panels with stars and crescent at their centres, and medallions with plant motifs inside.

Behind main dome of the structure is a floor mosaic made of multicoloured marble in opus sectile style.

Frescoes that form the major part of the decorations in the Museum usually depict Bible scenes. Basic depiction on the dome is the Pantacrator Jesus Christ reflecting his heavenly aspect. Behind this is a part with inscriptions, and lower is a frieze of angels. Moreover, 12 disciples are portrayed on the spaces between the windows. Pendentives include various compositions such as Jesus’ birth, baptism and crucifixion and the doomsday.

The vaults of the museum include similar biblical depictions. On the back arches of the structure are portrays on the circular medallions.