During that period the Nicene faith was preached by Gregory of Nazianzus only in a small chapel, subsequently dedicated to S. Anastasia.[127] But with the accession of Theodosius the Great the adherents of the Creed of Nicaea prevailed, and the Second General Council, held in Constantinople in 381, adopted that creed as the true faith of the Christian Church.

According to the biographer of S. Stephen the Younger, who enumerates the six ecumenical councils, and indicates, in most cases, where each met, that famous Council met in the church of S. Irene.[128] But Theodore Lector[129] says the Council assembled in the church of Homonoia, and explains the name of that church as commemorative of the harmony which prevailed among the bishops who gathered there on that occasion. As a matter of fact, one of the churches of the city bore the name Homonoia.[130] Possibly the discrepancy between the statements of the authors just mentioned may be due to a confusion arising from a similar meaning of the names of the two churches.

According to the Anonymus,[131] the usurper Basiliscus took refuge with his wife and children in S. Irene, when he was overthrown in 477, and the Emperor Zeno recovered the throne. But, according to the Paschal Chronicle,[132] Basiliscus fled on that occasion to the great baptistery of S. Sophia. As that baptistery stood between S. Irene and S. Sophia and may have served both churches, the difference between the two statements is not serious.

After standing for two centuries the Constantinian edifice was burnt to the ground by the fire which the rebel factions in the Nika Riot set to the offices of the prefect on Friday, the 16th of January 532. The building had narrowly escaped the same fate in the fire which destroyed S. Sophia earlier in the course of the riot, and might have survived also the conflagration in which it actually perished, but for the strong wind which carried the flames from the praetorium to the church, devouring on their way the bath of Alexander, a part of the hospice of Eubulus, and the hospital of Sampson with its patients.

The restoration of the church was included in the magnificent scheme of Justinian the Great to build on the wilderness of ashes created by his rebel subjects the finest monuments of his empire. And so S. Irene rose from its ruins, the largest sanctuary in Constantinople, except S. Sophia.[133] The bricks bearing the mark 'the Great Church,' Μεγάλη Ἐκκλησία, which are built into a raised bank against the northern wall of the atrium, afford no indication of the date when S. Irene was rebuilt. The bank is of comparatively recent origin.[134]

In the month of December 564, the thirty-seventh year of Justinian's reign, another great fire threatened to destroy the buildings which that emperor had erected in the quarter of the city beside S. Sophia. The hospital of Sampson was again burnt down; the atrium of the Great Church, known as the Garsonostasion, suffered; two monasteries close to S. Irene perished, and, what most concerns us, the atrium and part of the narthex of S. Irene itself were consumed.[135] How soon these injuries were repaired is not recorded.

During the 176 years that followed the reconstruction of the church by Justinian, S. Irene does not appear in history. But in 740 it was injured by the earthquake which shook Constantinople in the last year of the reign of Leo III. the Isaurian.[136] Theophanes[137] is very precise in regard to the time when the disaster occurred; it was on the 26th of October, the ninth indiction, on a Wednesday, at eight o'clock. The damage done both in the city and in the towns of Thrace and Bithynia was terrible. In Nicaea only one church was left standing, while Constantinople deplored the ruin of large portions of the landward fortifications and the loss of many churches, monasteries, and public monuments. S. Irene was then shaken, and, as the examination of the building by Mr. George has proved, sustained most serious injuries. The Emperor Leo died about six months after the disaster, and it is therefore uncertain whether the church was rebuilt before his death. His first attention was naturally directed to the reconstruction of the fortifications of the city, where his name still appears, with that of his son and successor Constantine Copronymus, as the rebuilder of the fallen bulwarks. But although there is no record of the precise date at which the ruined church was repaired, we may safely assume that if the work was not commenced while Leo III. sat upon the throne, it was undertaken soon after the accession of Constantine Copronymus. S. Irene was too important to be long neglected, and was probably rebuilt during the ascendancy of the iconoclasts.

The church reappears for a moment in 857 during the dispute which raged around the persons of Ignatius and Photius as to which of them was the lawful patriarch. While the partisans of the latter met in the church of the Holy Apostles to depose Ignatius, the few bishops who upheld the claims of Ignatius assembled in S. Irene to condemn and depose Photius with equal vehemence.[138]

The church comes into view once more in connection with the settlement of the quarrel caused in 907 by the fourth marriage of Leo VI. the Wise. As the union was uncanonical, the Patriarch Nicholas deposed the priest who had celebrated the marriage; he, moreover, refused the Communion to the emperor, and treated Zoe, the emperor's fourth wife, as an outcast. For such conduct Nicholas lost his office, and a more pliant ecclesiastic was appointed in his place. The inevitable result followed. The religious world was torn by a schism which disturbed Church and State for fifteen years. At length Romanus I. summoned a council of divines to compose the agitation, and peace was restored in 921, by a decree which condemned a fourth marriage, but allowed a third marriage under very strict limitations. So important was this decision regarded that it was read annually, in July, from the pulpit, and on that occasion the emperor, with the patriarch, attended service in S. Irene, and at its close took part in a procession from S. Irene to S. Sophia, on the way back to the Great Palace.[139]