The Chora consists of five main architectural units, namely the naos, the two-storied structure (annex) added to the north, the inner and the outer narthexes and the chapel for tombs (parecclesion) to the south.

The main structure of the existing church is a building on an athropied Greek cross plan covered by a dome. The dome is a ciborium-shaped high frame supported by four columns. 16 long windows provide lots of daylight to the interior. On each side of the bema, the eastern extension of the naos, were domed chambers called pastophoria. The chamber to the north (prothesis) directly opens to the bema, whereas the chamber to the south (diaconicon) had opened to the bema, but after the renovations in the 14th century, it was covered with marble and opened to the parecclesion. South to the naos is a passageway linking the naos to the parecclesion. The additional building (annex) adjacent to the north side of the naos is two-storied, and most probably, the lower story was housing the treasury (Skeuophylakion) and the upper story the library of Metochites. The units south and north to the inner narthex located west of the naos are covered with domes, whereas other units are covered with vaults. The section in the southwest of the outer narthex, where the bell tower was located earlier, houses the minaret today.

The main room of the church (naos) has a size of 10.5 m x 15 m. The apse is supported with an outer semi-circular flying buttress constructed in the Palaiologan period. The main room’s floor and walls are covered with marble. Inside the apse is the mihrab made in the Ottoman period. Stained glass pieces discovered during archaeological excavations at the apse section resemble those in the Monastery Church of Christ Pantocrator, and this is quite important because it indicates that the art of stained glass had been developed earlier in the Byzantine Empire than it had been done in Europe. The walls of the naos are decorated with valuable marble plates up to the cornice level, the narthexes are entirely decorated with mosaics, and the Parecclesion is decorated with frescoes.

The parecclesion adjacent to the south side of the naos was entirely built in the 14th century. This structure, which was built by Metochites as his own tomb chapel, included the tombs of Metochites, the founder of the monastery, and some people close to him. This elongated rectangular and single-nave structure has a size of 15.96 m x 4.96 m. The parecclesion is separated from the outer narthex by two columns that have capitals decorated with winged angels, crosses and acanthus leaves, and constitutes a whole independent from the narthex in terms of both architecture and function. As indicated by the four arcosolia for tombs in the parecclesion, this section was built upon a basement, which was used as a crypt and cistern as well, as a tomb chapel. The depictions in the 29 m long parecclesion were made as frescoes. The bema and apse section to the east is covered with a domical vault. There are four arcosolia for tombs in the parecclesion, two on the northern wall and the other two on the northern wall. An arched passage close to the bema arch of the northern wall leads to the chamber of diaconicon. On the east side of this rectangular structure, which has a size of 4.33 m x 3.21 m, is a small, semicircular protruding apse. The central part of the parecclesion is covered with a dome. This dome is 4.7 m in diameter and 11.18 m in inner height. The dome structure with 12 ribs (dodecagonal) is supported by a relatively high trimmer and has 12 windows. The space, which had been formed because of the construction of the parecclesion in the 14th century, between the parecclesion and the naos, was utilized by adding two chambers on either sides of the hole connecting the naos and the parecclesion. There are no frescoes or mosaics in these two chambers, which could have been utilized as storage rooms for liturgical articles or as small chapels (oratorium). Those chambers are thought to have been used to store materials such as candles, candelabras, incenses, icons and containers used during religious and memorial services carried out in the chapel. There are totally eight tomb arcosolia in Chora; four in the parecclesion, one in the north wall of the inner narthex, and three in the west wall of the outer narthex. Those tombs belong to aristocratic families. Additionally, beneath the apse decoration of the parecclesion is another tomb dating from a later period. 

Round arches, niches, stone walls with brick dog tooth eaves, and half-piers covering the facade of the building have provided a vivid outlook to the structure.