The Pammakaristos was either built or renovated to a large extent by Michael Tarchaniotes Glabas, protostrator of Andronicus II Palaeologus (1282-1328). Many historians and archaeologists, however, believe that the original structure was older and some attribute it to Michael VII Ducas (1071-1078). What is certain is that Tarchaniotes was the founder of the elegant parecclesion added to the south side of the church. It has also been suggested that the original building was erected in the 8th century (Mamboury). In earlier times there was a fragmentary inscription in the sanctuary, reading "Iwannou frontisma" ("taken care of by John"), but no one has been able to discover to whom it refers. George Pachymeres writing on Tarchaniotes remarks that the Pammakaristos was "his own monastery".
Historical evidence reveals the importance of this religious centre, which housed the Ecumenical Patriarchate from 1456 to 1587.The Pammakaristos remained in the hands of the Orthodox Greeks even after the Conquest. It is believed that the famous meeting between the Patriarch Gennadius Scholarius and Mehmet 11 the Conqueror and their discussion on questions of religion, took place here. When, three years after the Fall of Constantinople, the Patriarchate was shifted from the Holy Apostles to the Pammakaristos (1456), the holy relics and other valuable possessions were transferred to the new see.
In the third patriarchy of Simeon I of Trebizond (1466, 1471-74, 1481-86), the local Synod denouncing the "pseudo-union" of Florence and regulating relations between the Orthodox and Roman Catholic Churches was convened in the Pammakaristos. Many travellers and scholars who visited Constantinople after the Conquest described with admiration the patriarchal church of the Pammakaristos . In 1587, Sultan Murad III (1574-1592), converted the church of St. Mary Pammakaristos into a mosque and called it Fethiye (= Victory) Camii, to commemorate the conquest of Georgia and Azerbaijan.

The Patriarchate and its sacred relics and vessels were then transferred in haste to the church of the Theotokos Paramythia.The monastic complex of the Pammakaristos was composed of two churches, built at the north side of a walled enclosure. A number of ancillary buildings (cells, halls, offices, etc.) completed the compound. Within this enclosure, the katholikon and the parecclesion have survived to this day. The church is laid out on the ambulatory plan with arcades enveloping and communicating with the three aisles to the north, west and south, and two narthexes to the west. The exonarthex and north perambulatory are barrel-vaulted. Four piers support the dome of the centre bay. The apse to the east was destroyed when the church was turned into a mosque in the years between 1587-1591.

The latter is known to have retired to the monastery where he died in 1306. The decoration of the parecclesion was completed by his wife. The surviving mosaics, cleaned and restored by the Byzantine Institute of America headed by P. Underwood, formed part of the iconographic programme. In the conch of the apse Christ Hyperagathos is portrayed seated on a backless throne, holding a closed Book of Gospels in the left hand and raising the right in benediction. To the left and right, the full-length figures of the Holy Virgin and St. John the Baptist are shown turning towards Christ in veneration. The Deesis is flanked by the Archangels Michael and Gabriel.
In the dome the central medallion with the half length portrait of Christ Pantocrator in attitude of benediction is surrounded by twelve Prophets (Moses, Jeremiah, Zephaniah, Micah, Joel,