There is no precise and clear information about the first foundation of Kariye. However, it is possible to talk about different opinions about the construction of the building. One of the most known views is that the monastery was built by Theodora I's uncle. In the anonymous biography of St Thedoros written in the ninth century, it is stated that the commander Thedoros, the uncle of Theodora, the wife of Ioustinianus I, received permission to establish a monastery in 530 and started the construction of the monastery after 536. However, the fact that there is no possibility that Theodora I was the uncle of a famous commander and that the famous historian Procopius, the famous historian of the reign of Emperor Ioustinian I (527-565), does not mention the Kariye monastery in his book describing the buildings and temples of the period does not support the accuracy of this view.

The other view is that the monastery was built by Krispos, a general of Heraclius.

Despite all these uncertainties, the monastery was first mentioned in written sources in the eighth century, when Patriarch Germanos, who died in 740, was buried here. Baktangios, who died in 742, was buried here. In the 9th century, the sanctity of the monastery increased with the burial of Theophanes, the metropolitan of Nikaia, who died in 845.

Significantly damaged by anti-painting opponents during the "iconoclast" period, the building was virtually rebuilt by the archpriest Michael Synkellos (814-846) from Palestine in 813 after the iconoclast period, and Synkellos was buried here after his death in 845.

From the middle of the ninth century until the first quarter of the eleventh century, there is no information about Kariye in the sources.

However, from the last quarter of the 11th century to the 12th century, the Kommenos built a new church over the almost completely destroyed monastery. Maria Doukaina, mother-in-law of the Roman Emperor Alexius II Komnenos (1081-1118), rebuilt it during this period, and it is not known how faithful it was to the ninth-century structure.

Like many other buildings of the Komnenos dynasty, this building was dedicated to "Christ the Saviour". Shortly after its construction by Maria Doukaina, the building underwent major repairs for unknown reasons. In 1120, Isaakios Kommenos, the younger son of Alexios I, had the monastery almost completely rebuilt.

During the 4th Crusade between 1204-1261, the Catholic Latins and Venetians invaded and looted this church as well as other churches, and Kariye was severely damaged and ruined. So much so that not even a single paper remained in the church, which was a cultural centre with its library until that day.

The 14th century is important as the period when the building reached its present form. This period, called the Palaiogos period, began with the return of Emperor Mikhael Palaiologos, who lived in exile while the city was under Latin invasion, to the capital in 1261 and lasted until 1453. During this period, the Empire did not have the financial means to rebuild the city, which had been devastated by the Latin plunder, and the Church and the Emperor were not in harmony. During the reign of Andronikos Palaiologos II (1282-1321), a devout Orthodox who succeeded Emperor Mikhael Palaiologos, despite the general poverty of the Empire, there were families with the means to support the arts and sciences. Theodoros Metokhites, who built Kariye in its present form, belonged to one of these families.

In 1316, the Emperor appointed Metokhites as 'ktetor' (bani) to restore the Monastery, and when the restoration of the Monastery was completed in 1321, he was honoured with the title of 'Great Logothete'.

The civil war against the emperor Andronicus II began in 1321 and lasted until 1328, when his grandson Andronicus III ascended the throne. Metokhites, who was exiled by the new emperor, returned to Constantinople with the help of his son-in-law, went straight to Kariye and became a priest by exercising his Kretor rights and lived under the name "Theoleptos the Priest". After his death, he was buried in Kariye.

The building, which was not damaged during the Conquest of Istanbul, was not used for a while after the Conquest of Istanbul. In 1511, 58 years after Mehmed the Conqueror's conquest of Istanbul in 1453, there was a lack of mosques to worship in the region because the Mihrimah Sultan Complex had not yet been built. Atik Ali Pasha, one of the grand viziers of Sultan Beyazid II (1495-1512), restored and cleaned the abandoned Kariye and converted it into a mosque in 1511. A madrasah was added next to the building, which was converted into a mosque and endowed. The madrasah built by Atik Ali Pasha adjacent to the Kariye Mosque is mentioned in Tezkiretü'l-bünyân and Tezkiretü'l-ebniye as "Ka'riye Madrasah in Sultan Selim".

Since the building known as "Atik Ali Pasha Mosque" or "Kariye Mosque" was opened for worship, the mosaics and frescoes on the walls were covered with a thin plaster 2cm thick. Without touching the original architecture of the building, a minaret was added to one corner and a mihrab was added to the interior of the south-east corner.

It is observed that the mosaics and frescoes were not scraped and destroyed, that the mosaics in the place of worship were covered with wooden covers at prayer times, and that the church was appreciated by the people. In his Travelogue, Evliya Çelebi refers to Kariye as "Kariye Mosque near Edirnekapı: It was once an artistic church". In addition, Ayvansaraylı Hüseyin Efendi, who wrote a book on the mosques of Istanbul in the 18th century, mentioned the original and preserved identity of the building by saying "Cami-i mezbur munkaliptir from the church".

When the traveller Gyllius came to Istanbul between 1544-1547, he visited Kariye and mentioned the beauty of the marble coverings on the walls of the Kariye Mosque. Again in 1578, the traveller Stephan Gerlach mentioned the mosaics and frescoes when he visited Kariye. In the eighteenth century, Jacques Dallaway also mentioned the mosaics. All these show the importance given to Kariye by the administrators and people of the period.

After the earthquake of 1766, the Kariye Mosque underwent an important repair, which is known to have been carried out by the architect İsmail Khalifa.

In 1860, the architect Peloppida Kouppas was commissioned to repair the building; some of the mosaics were cleaned and the depictions were covered with wooden covers and curtains.

In the 1894 earthquake, the honeycomb part and the cone of the minaret of the building, which was damaged once again, collapsed in the earthquake, and the collapsed cone was completed in the classical style after a short time.

Again in this period, a wooden porch was built in front of the building. The building was restored again by Abdülhamid II in 1898.

The Kariye Mosque, which was used as a mosque for about 450 years, which became a large collection of buildings together with the madrasah, lodge, fountain and tomb built around it after it became a mosque, was turned into a museum in 1945 with the decision taken by the Council of Ministers on 2 August 1945.

The building, whose maintenance work was completed by Cahide Tamer, one of the architects of the Directorate of Foundations between 1945-1946, was given to the Byzantine Institute of America and Dummbarton Oaks Reserch from 1947 to 1958 for restoration work. During this restoration work, which lasted 12 years with a team consisting entirely of foreigners under the presidency of Paul Underwood, the artefacts from the Ottoman period inside the temple and all the parts belonging to the mosque were removed from the structure. Even the Ottoman hexagonal pavers of the outer narthex and paraclesion were removed.

In August 2020, it was decided that Kariye, which has existed as a museum and museum warehouse for 75 years, would be transferred to the Presidency of Religious Affairs with the decree of President Recep Tayyip Erdoğan and reopened to worship, like Hagia Sophia.

The Presidency of Religious Affairs, which took over the management of the Kariye Mosque by decree, started to work to make the building suitable for worship, and first of all, the pulpit, which was used to read the sermon during worship, was made of wood in accordance with the dark colours of the building and traditionally placed on the right side of the mosque.

When the ongoing restoration works are completed, it will be possible to worship in the Kariye Mosque, which is another milestone in terms of historical culture of Istanbul, just as the Hagia Sophia was opened to worship as a mosque.