Late Roman/Byzantine

The early-Roman residential quarter, discovered behind the mosque, was replaced during the 3rd or 4th century by an imposing building, possibly a basilica erected in line with the nearby temple.
This proves that the Sebasteion was still functioning then. And so was the temple of Kybele in 362 where the emperor Julian, on his march from Constantinople to Antioch, sacrificed on the altars of the Magna Mater and wrote his prose hymn for the Goddess in a single night in June.
He tried to revitalize her cult, which had obviously been in decline, although the territory of Pessinous must still have contained a considerable number of pagan villages.

It is clear that Christianity's hold was rather strong at that moment. The first certain Christian testimony dates from ca. 250, while several other inscriptions date from 350. Archaeological finds with Christian symbols and eulogy ampullas are more frequent from the 5th century onwards. The pagan villages around Pessinous probably began to accept the new religion in the 5th century as did the community living on the top of the Mount Dindymos where the ruins of a Byzantine fortress or fortified monastery are to be seen.

In 366, during the course of the civil war against the usurper Prokopios, the emperor Valens placed a strong military garrison in Pessinous.
When Galatia was divided in 399 under Eutropios, Pessinous became the political and religious metropolis of the new eparchy Galatia II or Galatia Salutaris (Salutaria). Its first known bishop Demetrios, ordained in 403, was a fervent follower of St John Chrysostomos. The names of its bishops can be found in the lists of the main religious meetings (councils and synods) held afterwards in the Byzantine Empire.

From the 6th until the end of the 12th or the beginning of the 13th century, Pessinous was occasionally called Joustinianopolis. The metropolite Georgios together with the domestici (leading citizens), local clergy and many common people were able to move St. Theodore of Sykeon (542-613) to bring an end to a draught in their city, causing however a flood of the Gallos in the western half of the town. At that time the main churches were the Haghia Sophia cathedral and the "Myriangeloi outside the walls".

To the former belong the two only preserved upstanding walls of the whole site, which has been located behind the mosque, which was built upon the "basilica" in the first half of the 6th century. Only the 5 m. deep foundations of the outer wall and a badly preserved monumental marble staircase leading to its entrance have been excavated.

Somewhat later at the end of the 6th century the whole area of the temple was transformed into a simple residential area with a road, while the square below was also covered with house quarters with workshops constructed from re-used materials.
The name of the latter church implies that the city was walled, which never was the case. Instead a system of watchtowers and strongholds were built on the hills and plateaus surrounding the inhabited valley.

The most conspicuous construction, a fortress revealing several phases of habitation, was erected in the first half of the 6th century on a site called "Akropolis" by 19th century travellers; it was previously used as a necropolis (2nd century B.C.- second half of the 5th century), one of the many scattered around the surrounding plateaus

Defended by a monumental wall, with watchtowers, the inner space consisted of a separately defended "dungeon" in the south and a dense housing sector in the northern part. While the dungeon held several larger buildings, most parts were rebuilt upon by small houses and some workshops.

Three such houses, which have been fully examined, have limestone walls, plastered on the inside and one entrance. They have only 1 or 2 rooms, often bearing areas for food storage: large pithoi and silos dug into the marly soil. Among the other provisions found in some of these houses are fireplaces, wall niches, cisterns for water collection and terracotta servers. The fortress remained in use until the 3rd quarter of the 11th century.

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To which extend Pessinous, - situated on the frontline between the often besieged and conquered cities of Amorium and Ankyra, the 2 main military centres of the Anatolian plateau - suffered from the incursions of the Arabs between 641 and 931, is unknown. An alleged conquest in 664 by Abdarrahman b. Halid seems unlikely. The metropolitan seat, however, was possibly moved momentarily during the 9th century to much safer (S)paleia to be identified with Sivrihisar, which is dominated by a powerful fortress, or perhaps with the fortified top of the Mount Dindymos.

Pessinous lost importance in favour of Amorium, which became the second metropolis of the province around 860.
When under the threat of invasions in the 7th century the Byzantine Empire was divided into new administrative and military "Themas", Pessinous belonged to the "Thema" Opsikion with had Ankyra as its capital while neighbouring Amorium was the nerve centre of the "Thema" Anatolikon.
A seal of Basileios II (976-1025) probably indicates the presence of a civilian institution.

When exactly Pessinous fell into the hands of the Seljuks after the battle of Manzikurt in 1071 remains unclear. While the most recent coins all date from the third quarter of the 11th century, as well as the most recent metropolites attested in the synods of Constantinople, Pessinous is still mentioned as a metropolis in the Notitiae episcopatuum in the 14th century.
Its ruin along with that of Amorium was probably complete during the early fourteenth century.