Having been separate from Imperial since the first Council of Ephesus (431), the Syriac Church of the East reappeared in Egypt after the Arab conquest, in particular during the Abbasid period, and Nestorians were used as employees. The Nestorians lived mainly in Cairo. Yahya ibn Sa‘id of Antioch, the Melchite patriarch of the 11th century, gives the first mention of a Nestorian community. He quoted the sack of two Nestorian churches on 29 March 961. In 996, the house of their bishop was sacked. During the reign of al-Hakim, a Coptic Church in a suburb south of and a Nestorian church within its vicinity were destroyed. Abu al-Makarim/Abu Salih mentioned that a Muslim rented a property from a Nestorian priest who belonged to the Nestorian churches.

There was a monastery mentioned by the same author south of Old Cairo. It was restored during the reign of al-‘Amir (1101-1130) and many monks came to dwell in it. By the year 1181, there were no more Nestorians in Egypt. The Copts bought this property during the patriarchate of Mark ibn and it was named after St. Philotheus of Antioch. In the year 1346, Nestorians were found in Damietta where they had a church named after the Virgin located next to the church of the Franks. They are mentioned as new arrivals to this city. There was also a Nestorian church in Alexandria but no other information exists.

Regardless of the theological conflict between the Copts and the Nestorians, the Coptic scholars and the Coptic hierarchy read many Nestorian authors, and among them is of Nineveh, who wrote several mystical works and was very appreciated by Coptic monks. In his book The Lamp of Darkness for the Explanation of the Service, Ibn Kabar mentioned several Nestorian authors, among them Amr Matta al-Tayrhani, who was contemporary to Ibn Kabar, and Elijah, metropolitan of Nassibin. Ibn al-Assal, one of the great Coptic scholars of the Middle Ages, also referred several times to Nestorian authors.