Isa Bey Mosque is situated on the southern slope of a hill overlooking modern Selçuk, just below the Ayasuluk Castle and the Basilica of St. John. It consists of two main spaces, the courtyard on the north and the narrow rectangular prayer hall on the south, measuring about 51 to 57 meters as a whole.
Isa Bey Mosque is one of the most important works of the Turkish Aydin Emirate (Aydinogullari) who ruled in western Anatolia from 1308 to 1426. It was built in 1374 by Aydinoglu Isa Bey (1360-1390) in his administrative capital of Selçuk, near Ephesus. It is the second example of the twin-minaret mosques in Anatolia from the pre-Ottoman principalities period and is larger than many of the mosques of the time. Its architect was Ali bin Mushimish, from Damascus. The mosque was repaired in 1934 and restored later in the second half of 20th century.


The main entrance to the courtyard is through the monumental portal on its western façade, which faces the sea, close to the prayer hall. It is set on a slope with a double staircase that features a large niche with a fountain under the landing. The entry recess has a muqarnas vault with an umbrella crown and bears a finely carved inscriptive plaque. A smaller portal is placed on the eastern façade, in line with the primary portal and a third is centered on the northern façade, facing the hill.
The courtyard has an octagonal fountain at its center with twelve freestanding cylindrical columns on three sides that are all that remains of the courtyard arcade. Many of the columns are in bad condition with deep cracks. While the minaret at the southeast corner of the courtyard has not survived, the octagonal base and cylindrical shaft of the southwest minaret remains up to its muqarnas balcony.

The prayer hall entrance is a triple archway at the center of the courtyard façade. The doorway is crowned with two arched windows on either side of a circular window. Inside, the prayer hall is two bays deep measuring 18 x 48 meters. Two domes supported by brick arches and four granite columns surmount the two central bays of the entrance and the mihrab. The mihrab dome is slightly smaller with a diameter of eight meters. Three of the four columns have traditional stalactite capitals, while the other bears a Roman composite capital. The interior is illuminated by two upper tiers of arched windows placed at regular intervals. The courtyard walls are similarly pierced with arched windows, except for the eastern one. The arched and rectangular windows flanking the main western portal are decorated with stained glass and thick carved stone frames.
The mosque walls are made of exposed rough stone, while the western façade is covered with fine marble panels and decorated with carved inscriptions, muqarnas and polychrome stone composition. Inside the prayer hall, the squinches of the mihrab dome are decorated with a mosaic of tiles with hexagons and star patterns in turquoise and navy blue. Plant motifs are also used in various decorations. The stalactite carvings on the octagonal drum of the dome are in the Seljuk tradition. Some of the upper windows on the qibla wall are decorated with stalactite frames.
Due to a long period of neglect followed by improper restorations, Isa Bey Mosque has lost many of its original properties. A door was cut through the qibla niche, and the muqarnas crown of the mihrab was taken to the Kestane Pazari Mosque in Izmir in the 19th century when the mosque served as a caravanserail. The mihrab niche was filled with stone masonry at a later date.