Although the exact construction date of the building is unknown, according to the description of Symeon the Metaphrast, an author and saint who lived in the late 10th century, the region where the Chora monastery was located began to gain importance as a holy cemetery (necropolis) when the relics of Saint Babylas, who had been martyred in the early periods of Christianity, in 298, together with his 84 disciples, in Nicomedia (İznik), were buried here in the early 4th century.

The Chora monastery was rebuilt in the 6th century, in 536, by the Emperor Justinian (527-565) on the cemetery that was considered holy, on a chapel that had been ruined. On the other hand, according to the unproven claim on the page 229 of the calendar of Byzantine feasts written by Manuel Gedeon, the construction of the monastery had been initiated by Theodoros, the uncle of Justinian’s wife Theodora, in the 6th century, but it had been devastated by an earthquake that occurred on October 6, 557, and the emperor had built a larger monastery on the site of the former one.

Afterwards, the monastery was used as a burial area for prominent persons. When the Patriarch Germanus who died in 740 was buried here, the monastery appeared for the first time in written sources, and its degree of holiness increased, when Theophanes, Metropolitan of Nicaea, who died in the 9th century, also was buried here. The building was destructed in the Iconoclastic period (711-843) and it was reconstructed in different periods. According to archaeological studies carried out between 1947 and 1958, there were five different construction periods here, and those periods witnessed in the 11th, 12th and 14th centuries should have been the periods of large-scale constructions or restorations.

The only surviving element originating from the earliest period of the building that lasted until the 9th century is the substructure on the east side. This substructure, which originates from the 5th or 6th centuries as indicated by its masonry, had not been built as a crypt, but it was used later as a burial place, as indicated by the tombs uncovered. At the end of the Iconoclastic period, after the Council of Nicaea in 843, Michael of Synkellos, who was appointed the high priest of the monastery, rebuilt the monastery completely by organizing a large construction campaign.

The remains of this structure built in the 9th century can only be seen today at the eastern end of the church. The tomb covered by a barrel vault beneath the naos covering dates from this period.

During the Comneni period (1081-1185), since the Great Palace was abandoned and the religious ceremonies were held in the Chora Monastery Church that was close to the new imperial residence at the Palace of Blachernae, the church gained in importance. In the last quarter of the 11th century, Maria Doukaina, the mother-in-law of Emperor Alexios I Komnenos (1081-1118), built a new church upon the ruins of the Chora Monastery. The remains of this building can be seen at the lover parts of the naos walls, under the marble coverings. Since almost no part of its superstructure has survived, the exact form of the building is unknown.

Isaac Komnenos, the younger son of Alexios I, rebuilt a large part of the monastery in 1120. The former three apses were replaced by a single and large apse, the relatively small dome supported by four columns was enlarged and supported by four corner pillars, the arches were narrowed, and thus, a more monumental interior space was created.

There is almost no information about the Chora Monastery during the Latin occupation between 1204 and 1261, but considering the large-scale construction of Metochites, the monastery seems to have been devastated during the Latin occupation.

It is known that the huge earthquake of 1296 devastated the monastery. Patriarch Athanasius I, who resided in the Chora Monastery in the early 14th century, mentions the very bad condition of the monastery.

During the reign of Andronikos II (1282-1328), although the empire experienced economic difficulties in general, there was also a community of wealthy aristocrats, which supported artistic and scientific activities. In this period, Theodore Metochites almost reconstructed the Chora Monastery and established a very large and rich library inside the monastery. For the Byzantine aristocracy, building or repairing a religious institution was considered as a source of prestige in this world, and as a very important investment for the afterlife, before God.

Theodore Metochites was the son of an aristocratic family, born in 1270 in Constantinople. His father served as Michael VIII Palaiologos’ ambassador at the Papacy. After the dethronement of Michael VIII in 1283, the Metochites family was exiled. During their period of exile, Theodore Metochites studied the Hellenistic trivium and quadrivium, and he was additionally trained in ancient philosophy and theology. In 1290, he was accepted to the court of Emperor Andronicus II, and he became a senator and the Logothetes, the Byzantine official responsible for the treasury, who was the highest official after the Emperor. He even established relationship with the imperial family by making her daughter marry Ioannes Palaiologos, the nephew of the Emperor. In 1316, he was appointed by the Emperor as ‘ktetor’ (donor) for the restoration of the Chora Monastery that was under the protection and directorship of the court. When the restoration of the monastery was completed in 1321, he was granted the title of Grand Logothete; i.e., the most important title granted by the court. This was stated via the gilded inscription on a green surface on the dyed capitals of the two marble frames of the large window in the southern typhanon of the naos. The inscription on one side of the left capital reads “ktetor”, the inscription on the other side of this capital reads “Theodore”, the inscription on one side of the other capital reads “logothetes”, and the inscription on the other side of this capital reads “Metochites”. Metochites was proud of the monastery he had built and of the large library he had established inside this monastery in particular. Although there is no definite archaeological evidence about the building of this library, both the poems of Metochites and the letters he sent to the priests of the monastery from exile indicate that there had been such a library inside the monastery. The library of the Chora Monastery is referred as one of the most important libraries of the Constantinople of the Palaiologan period.

The renovations undertaken by Metochites were comprehensive. The main dome of the church, the two-storied structure (annex) added to the north, the inner and outer narthexes and the chapel (parecclesion) added to the south, and additionally the marble covering plates and mosaics of the naos, the mosaic decorations of the narthexes and the frescoes of the additional chapel were built by Metochites.

Metochites, who was a senior bureaucrat, wanted his reputation to survive after his death. His choice of rebuilding the Chora Monastery and furnishing its library indicates that as a good Christian, he was worrying about the afterlife as well. The rich library was both to transfer his reputation in this world to the next generations and to make him appreciated by God thanks to his great good work.

Metochites was a good Christian, but not a sectarian. He carefully avoided conflicts with the church. He did not prefer to discuss religious issues, and confined himself to being faithful.

When Emperor Andronikos II was dethroned in 1328, Theodore Metochites was forced into exile in Didymoteicho, Thrace, by the new emperor, lived two years in exile, and he described his painful experiences and exile years in his poems that had very complicated literary plots.

When he was allowed to return to Constantinople with the help of his son-in-law in 1330, he went to the Chora Monastery and became a priest using his rights as the ktetor of the monastery. He died in 1332 in the Chora Monastery and buried in the grave niche in the parecclesion south to the church.

Metochites was not only successful in the areas of literature and politics, but also in developing architectural solutions for the Chora Monastery Church, in decorating the monastery with brilliant and harmonious mosaics and frescoes, and in organizing religious depictions in a chronological order and iconographically. In this respect, he might be considered as the pioneers of a new art movement in the Byzantine Empire, which was the contemporary of the Renaissance movement initiated by Giotto (1266-1337) in Italy.

Another feature distinguishing the Chora Church from the other churches of this period is the depiction of the scenes from the life of Virgin Mary in chronological order by using the Apocryphal Gospels, although these scenes are not included in the four Canonical Gospels. Metochites added a mystical meaning to the name of the church, ordered the mosaic on the entrance gate that is depicted as “Chora (uterus, in the Latin language), the container of the uncountable, the place where Jesus Christ fit into the uterus, where he incarnated”, dedicated the church to Virgin Mary, and explained this in one of his poems as well.

In 1453, when Sultan Mehmed II the Conqueror (1451-1481) conquered İstanbul, the church suffered no damage. After serving as a church for any years, it was converted into a mosque during the reign of Sultan Bayezid II, by the Grand Vizier Hadım (Eunuch) Ali Pasha (Atik Ali Pasha), and a madrasah (school) was added next to it. In the Turkish period, the monasteries except this church were ruined and disappeared in the course of time.

Besides the reconstruction of the demolished dome and the repair of some damages caused by earthquakes, the windows of the outer narthex were covered largely and a mihrab was added to the naos. The sarcophagi in the tomb arcosolia were removed.

According to the descriptions of travelers who visited this building, while it was serving as a mosque, the mosaics of the building were covered with removable wooden shutters.

In the first half of the 18th century, a school and a soup kitchen were added to the building by Kızlarağası (“Chief of the Girls”) Hacı Beşir Pasha (d. 1746). However, these annexes have not survived.

The Chora Mosque was converted into a mosque upon the decision of the Council of Ministers dated 29/08/1945. This monumental museum, which is called the Chora (Kariye) Museum today, is a quite attractive Eastern Roman building with both its architecture and its mosaics and frescoes.