Stoudios Monastery (later known as İmrahor Mosque) was located in the Psamathia region of Constantinople near the Golden Gate, just south of the Mese. Dedicated to St. John the Baptist (the Prodromos), the monastery was founded by a Patrician named Stoudios in the mid 5th century, making it the oldest church in the city. It has been suggested that it was originally built to house the head of John the Baptist, which was discovered discovered in 453 (though it ended up in the Monastery of Akoimetoi). 
While it is currently in ruinous condition, the surviving structure of Stoudios Monastery is the oldest church in Istanbul. It was a large 5th-century three-aisled basilica, preceded by porticoed atrium and a narthex (divided into three bays) to the west and a single apse at the east end. The nave was flanked by green marble columns with acanthus capitals. The monastery would have been richly decorated, as seen in a relief of the Entry into Jerusalem. It has opus sectile pavement with figures of animals and mythological scenes, probably dating to the 11th century (thus comparable to the Monastery of the Pantokrator). The semicircle of the apse, which was polygonal on its exterior, contains the remains of a synthronon. A cruciform crypt was uncovered under the apse, which probably once housed the monastery’s relics. A small chapel (possibly dating to the Late Byzantine era) was recorded at the beginning of the 20th century, which has since disappeared. 

To the southeast of the building is a cistern perhaps dating to the 5th century. It has a trapezoidal plan (26.4 meters by 18.6-16.65 meters). It had 24 granite columns (6 x 4 at regular 39 meter intervals) with Corinthian capitals. In 1970 a fire destroyed much of the cistern. To its east is an hagiasma. The cistern, which perhaps dates to the 5th century, has a trapezoidal plan (26.4 meters by 18.6-16.65 meters). It had 24 granite columns (6 x 4 at regular 39 meter intervals) with Corinthian capitals. In 1970 a fire destroyed much of the cistern. To its east is an hagiasma.

The monastery first played a significant role in the religious and political life of Constantinople during Iconoclasm during which it was a bulwark of support for image veneration under the leadership its abbot (hegoumenos) Theodore of Stoudios (759-826). Several sources, including documents written by Theodore, provide information on the organization of the monastery. Records mention as it as having many as 1000 monks at one time, though there are reasons to doubt this high figure. Nonetheless, no contemporary monastery came near to matching its size. The monastery attempted to be self-sufficient. It possessed lands, gardens, vineyards, water mills, livestock, a wharf with boats, workshops. The monks had to work on the land or in workshops, in the kitchen or refectory, to fish or to tend livestock. By the early 9th century, the monastery became a center of intellectual activity, where hymnography and a scriptorium flourished, thus helping give rise to a sort of renaissance in the ninth century. An example of this can be seen in the Theodore Psalter now at the British Library. The rules of Theodore served as a model for the organization of several monasteries, including some on Mount Athos. 
In the political struggles of the 9th century, Stoudios maintained an independent position against both the emperor and the patriarch. The monastery also served as a place of confinement for unsuccessful rebels and deposed emperors, including Michael V Kalaphates, Isaac I Komnenos, and Michael VII Doukas. It played a lesser role under the Komnenoi and entered a period of decline during the Latin occupation of Constantinople. It was restored in 1293 and in the 14th century held first place among the monasteries of Constantinople. It was converted into a mosque by İlyas Bey, the mirahur (stable master) of Bayezid II, hence its Turkish name. It underwent extensive alterations during the Ottoman Era. It was devastated by an earthquake in 1894, severely damaging what remained of the monastery. It was partially excavation by the Russian Archaeological Institute in 1907-09, which uncovered the opus sectile pavement, the crypt under the apse and burials in the south aisle.