Architecture 
The north church is the earliest securely dated Middle Byzantine church and the earliest example of the cross-in-square type in Constantinople. The naos measures approximately 12 x 10 meters and is divided into nine bays. To the east of the naos is a tripartite bema and to the west a three-bay narthex. A narrow exterior porch originally covered the main entrance to the narthex. The four columns that used to support vaults were replaced by pointed arches in the Ottoman Era, but three column bases have remained in their original positions. In the central bay there was a dome, which collapsed or was seriously damaged in one of the fires and was replaced during the Ottoman Era. The north and south vaulted arms of the cross-in-square core terminate in huge triple windows on the north and south façades.
The most distinctive features of the north church were its six additional chapels, all part of the original design. Two single-nave chapels flanked the prothesis and diakonikon at ground level. The north one has disappeared, but a portion of its apse foundation has been excavated. The southern chapel, located next to the diakonikon, was incorporated in the thirteenth century into the south church of Saint John to serve as its prothesis and thus was partially preserved. Both chapels were slightly larger than the rooms to which they were attached. On the roof of the north church are four chapels, which are not visible from the interior. The two quatrefoil western chapels are situated over the western corner bays of the naos. Two more chapels are located over the diakonikon and prothesis at the east end of the building. Access to the roof was through a staircase inside the tower south of the narthex.

The masonry of the south church and ambulatory are the same: approximately five courses of brick alternating with three or four courses of dressed stone, each course of stone separated from the next by one or two courses of brick. Its central core, a simple domed square bay, is enveloped on three sides by an ambulatory. The east side of the domed core extends into the bema with an apse, seven-faceted on the outside. The marble floor of the bema has been preserved. The rest of the floor in the naos was paved in the opus sectile technique. The walls and vaults were covered with mosaics. The ambulatory is lower than the domed core and the bema, providing the access of light into the central space of the naos through triple-windows on three sides of the square core. The naos is preceded by a narthex, originally covered by a dome. The narthex and the ambulatory were filled with tombs, leaving the central domed core to function as the main liturgical space.
One of the most striking aspects of the complex was the abundance of burials of different types within the monastery: twenty-nine tombs, along with four ossuaries. The tombs were placed in arcosolia, built along the outer walls of the perambulatory. The interior was painted with frescoes, as suggested by fragments preserved in the westernmost arcosolium of the perambulatory's south arm. The façades, in their rhythm of stepped pilasters and doors, closely follow those of the two churches.
The north church provides probably the largest and the most outstanding collection of Middle Byzantine sculptural decoration in Constantinople. Original decorated window mullions, leveled cornices, corbels are still found in situ. The ornamental repertory consisted of foliage, palmettes, fantastic plants, rosettes, crosses, peacocks, and eagles. These provided inspiration for similarly decorated mullions and cornices for the south church, but they are simpler and less precise in carving.
A great number of fragments of ornamentally carved slabs, cornices, archivolts, sculptured eagles, inlaid plaques, and glazed tiles were found in the excavations of 1929 and 1960s. Among these, there was a complete 10th-century inlaid icon of St. Eudokia. The glazed tiles, with painted floral and geometric ornaments, also belong to the 10th century and were probably used as borders and frames. A group of fragments with sculptured busts of the Apostles belonged to an archivolt, probably carved for one of the arcosolia.