The monastic complex was built near the Golden Gate, in the city's district known as Psomathion, and the katholikon was consecrated to St. John the Baptist. Many historians, chroniclers and travellers have recorded facts and events related to the monastery of Studius-among them Theophanes, the authors of Theophanes. Continuatus, Leo Grammaticus, Michael Attaleiates, George Acropolites, George Cedrenus, George Codinus, Michael Glycas, Nicetas Choniates, Nicephorus Gregoras, Symeon Metaphrastes.
The monastery's history is supplemented by various sources and documents, such as resolutions and acta of councils and even official correspondence. In later times the monument has been the object of study by E. Van Millingen, J. Ebersolt, A. Thiers, Ch. Pertusier, A. Paspatis. A list of the main incidents in the eventful history of the monastery is given below. The material is vast and it is regrettable that the 3-volume research work on the history and architecture of the Studius Monastery prepared by Nicephoros Eleopoulos has not been published, except for the smaller contributions on its Library and Scriptoria.
463 The monastery is founded by the Patrician Studius. During the Iconoclastic period the monks are persecuted and the monastery is closed. Theodore the Studite (759-826) leads the struggle for the restoration of icon veneration and with his powerful personality becomes an unrelenting opponent of the Iconoclasts. Leo Grammaticus calls him "fervent champion of Orthodoxy". Theodore organized the monastery, encouraged theological and philosophical studies, set up a school for the education of children, and founded hospices for the destitute and the travellers.

During his abbotship the monastery's scriptoria, directed by his uncle Plato, flourished. Many of the illuminated manuscripts produced by the numerous painters and copyists, miniaturists and calligraphists, are now in the Libraries of Western Europe (Cod. Venet. 555 of the 11th century, Cod. Vatic. gr. 831, Cod. Vatic. gr. 1671 of the 10th century, etc.). The names of four copyists are known: the monk John (916), the deacon Dorotheus, the ecclesiarch Eulogius (l0th century), the abbot Cosmas (l0th century). Manuscripts and icons produced in the monastery of Studius were in demand through out the Christian world. Three erudite monks of Studius acceded to the Throne of the Ecumenical Patriarchate: Antony III (974-980), Alexius (1025-1043) and Dosithe (1191-1192). In the reign of John I Tzimisces (969-976) the first typikon for Mount Athos was compiled by Euthymius the Studite.

Antony of Novgorod (1200), Stephen of Novgorod (1350) and de Clavijo (1402) have described the church marvelling at the size of the monastery and its astonishing beauty. They comment on the vast expanse of the vineyards, the abundance of water, the beautiful gardens extending almost as far as the Golden Gate, and give details on the mosaic decoration of the walls and floor of the church.
After the Conquest, in the reign of Beyazit II (1481-1512), the monastery of Studius was ceded to the Albanian Ilyas Bey, the Sultan's Emir ahir (Stablemaster), who converted the church into a mosque hence known as Imrahor Camii, a corruption of the words Emir-ahir Camii (i.e. Mosque of the Stablemaster). The destruction of the historical and once influential monastery started with the fire of 1782. Its dilapidation was accelerated by the damages caused by earthquakes in 1894. Finally, the great fire of 1920 ruined it completely.