After the appointment of Metochites in 1316 by the emperor as the ‘ktetor’ (donor) to restore the Chora Monastery under the protection and direction of the palace, the restoration of the monastery was completed in 1321. The main dome of the church, the two-story additional building (Annex) adjacent to the north side, the inner and outer narthexes and the additional chapel to the south (parecclesion), furthermore the marble plates and mosaics of the naos, the mosaic decoration of narthexes and the frescoes of the additional chapel had almost their present-day appearances. After these renovations undertaken in the 14th century, the chamber in the south (diaconicon), that had been opening into the bema, was closed with marble and began to open into the Parecclesion.

After the earthquake of 1766, the main dome of the church that had collapsed was renovated by the architect İsmail Halife. During this renovation, the original 14th-century dome was replaced by a wooden dome covered with plaster.

In the reign of Sultan Abdülaziz, between 1875 and 1876, the mosaics were cleaned and uncovered by the Greek architect P. Kuppas and some changes were applied to the facade of the building. The fillings made by pouring stone chips between domes in order to cover the narthex with lead had adverse effects on the appearance of the building and increased the weight of the structure. In 1898, Sultan Abdülhamid II had the building, which had been damaged and the minaret of which had been destroyed by the earthquake of 1894, restored. During the partial restoration undertaken in 1929, the Koimesis mosaic in the naos was cleaned and uncovered. During this restoration, some of the additions in the interior made during the Turkish period were removed and the minbar, which has reached the present day, was sent to the Zeyrek Mosque (Church of Christ Pantocrator). After 1948, the building was attached to the Administration of Museums.  

Between 1947 and 1958, a comprehensive cleaning and restoration program was implemented under the leadership of Thomas Whittemore by the ‘Byzantine Institute of America’ and the ‘Dumbarton Oaks Research Institute’. The frescoes and mosaics displaying the characteristic features of the 14th century were uncovered and the building obtained its current appearance.