[4] After the death of his wife, shortly after 1134, Emperor John II Komnenos built another church to the north of the first one which was dedicated to the Theotokos Eleousa (Merciful Mother of God).

[3] By 1136 at the latest a southern courtyard and an exonarthex were added to the complex,[3] and the two shrines were connected with a chapel dedicated to Saint Michael,[5] which became the imperial mausoleum (heroon) of the Komnenos and Palaiologos dynasties.

[4][dubious – discuss] During the period of Latin domination after the Fourth Crusade in 1204, the complex fell into the hands of the Venetian clergy, and an icon of the Theotokos Hodegetria was housed here.

After the completion of the medreses in the Fatih complex in 1471, Muslim students abandoned Zeyrek,[9] and the rooms once occupied by the school vanished.

[4] By the early 21st century the edifice had become very rundown and partly ruinous as a result of which it was added to the UNESCO watchlist of endangered monuments.

[13] The south and the north church are both cross-shaped with central domes and polygonal apses with seven sides rather than the five that had been typical in the Byzantine architecture of the previous century.

The historical opus sectile floor made from coloured marble worked in a cloisonné technique, with human and animal figures represented, is currently covered by a modern carpet.