The Eflatun Mescidi, the converted Byzantine church of Ayios Amphilochios, used to share the hill with the mosque before the 1920's.

The eastern wing of the mosque, its pillars constructed with re-used Byzantine columns and capitals, is unusually open and spacious.

The minaret, the marble mihrab (1891) and the eastern door, through which most visitors enter the mosque, date from the Ottoman period.

The courtyard of the mosque contains two typically Seljuk tombs (kümbets), one built by Kilicarslan II and still retaining some blue tiles on its roof.

Over the main entrance to the mosque an inscription attributes its completion to Sultan Alaaddin Keykubad I in the year 617 H (1220–221).

According to an inscription on its façade, Kilijçarslan II commissioned a ten-sided tomb with a conical roof[12] which became the burial place of the Seljuk dynasty, housing the sarcophagi of eight of the Seljuk Sultans of Rum: A second octagonal mausoleum was begun by Kaykaus I but was still unfinished at the time of his death in 1219.

Until 1951, the mosque was administered by the General Directorate of Pious Endowments (Vakıflar Genel Müdürlüğü).

[14] During a four-year restoration process lead sheets and heavy concrete slabs with waterproof layering were laid over the dome of the western section.