The earliest archaeological remains at the site date to the Hittite era of the 2nd millennium BCE, when the site was known as Apasa. There is also evidence of some Mycenaean presence before the start of the Helladic period around 1050 BCE. The hill is known to be the original location of Ephesus, before it moved to a new location a few kilometers away.

As with the outer fortifications the citadel walls were built with rubble stone and are strengthened with fifteen towers. The citadel of Selçuk has two major gates, one on the eastern side and the other on the western flank.

The castle was built during the Byzantine era (circa 6th century CE), however the current fortifications vear traces of Aydinid and Ottoman Imperial era reconstructions as well. Thecity walls of the inner castle made ofrubble stones.

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Selçuk Citadel
The citadel is located on the highest point of the Ayasuluk Hill, to the north of the Church of Saint John. The rocky platform on which the structure of the citadel is situated forms the upper most part of the Ayasuluk Hill. The fortress of Selçuk bears a long and very active history. The walls seen today belong to the Seljuk and Ottoman periods. The citadel enclosed several important structures including a royal palace, water-cisterns, a small mosque and residential houses for notable people.

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Mosque of Isa Bey
The Isa Bey Mosque (İsa Bey Camii) is one of the most delicate examples of Seljukian architecture, situated below the basilica of Saint John. The mosque was built by the master Syrian architecture Ali son of Mushimish al -Damishki, between the years of 1374 and 1375. The mosque was styled asymmetrically unlike the traditional style, The location of the windows, doors and domes were not matched, purposely. In the entrance of the mosque, an inscription from the god decorates the doorway. The columns inside the house of prayer are from earlier ruins in Ephesus, making an interesting contrast to the mosque. The domes are ornamented by turquoise and blue faience, revealing the characteristic of Ottoman style. Crown-like doors from Seljukian architectural style later combine with the specific decoration elements of architectural style.

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Church of Saint John
The Church of Saint John is very important, both for its unique ritual and architectural arrangements and for its acknowledged resemblance to the Church of the Holy Apostales in Constantinople (modern day Istanbul). In the Fourth Century CE, a great basilica was built over the tomb of Saint John by the Roman Emperor Constantine. Later, in the Sixth Century CE, an even larger and more magnificent basilica was built over the earlier structure on orders of the Roman Emperor Justinian, who ruled from 527–565 CE. The Emperor Justinian and his wife Theodora made large financial contributions and her name was inscribed over the big capitals which crown the beautiful marble columns.

This great basilica was known as the Justinian Basilica to honor the burial place of the Apostle Saint John who came to Ephesus in company with the Virgin Mary. It contained six 95-foot high large cupolas that covered the main aisle. It has been determined that if fully restored it would be the seventh largest Cathedral in the world. Saint John was so honored that the size of the basilica might have been larger if it were not for the limitations of the Topographical Area.

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Gate of Persecution
The main gate called "Gate of Persecution", located to the south of the building complex has remained as the most intact portal among all the entrances to the acropolis complex. Thegate hassquare-plan towers on both sides and an arched entrance portal at the center. the upper section of the arch contains a sarcophagus-like surface relief of Eros. Beside this, there were other relisfs (found until 1800s) about the prosecution scene of Hector and Achilles.Reliefs were removed to England in 1812 CE and put on display in the Woburn Abbey Gallery.

Some of the faded relief-frescoes still remain at the upper part of the arch. There are three medallions in the curly branch along upper part of the arch. There are possible depictions of prophets and saints in three aureoles fields. On the side of the frames there are two rectangular fields as well, depicting figures seeking east and west. Jesus is also depicted in the middle with his seven apostles. These frescoes have been dated to the 8th century CE or later.