The conquest of Egypt had immeasurable consequences for the Coptic Church. On the eve of the invasion, Emperor appointed Cyrus (known to the Arabs as al-Muqawqas) as both and ecclesiastical head. He persecuted the as well as their patriarch, Benjamin, who had to flee to for 13 years. Thus the had little motivation to support the army. However, there is no evidence for their cooperation with the Arabs during the actual invasion between the end of 639 and the capture of the Fortress of in 641.

After an armistice of 11 months to evacuate the forces and Greek civilians, the great city of Alexandria opened its doors to the Arabs and immediately lost its position as a most important cultural city. Although the army under General ‘Amr ibn al-‘As was much less in number than the garrisons, it achieved a relatively rapid expansion in Egypt. By that time, the forces in Egypt were ill equipped and trained to operate in the manner of police than as a militia.

The condition for making peace with the countries being invaded by the Arabs was to choose one of three options: paying the poll tax (jizyiah), to Islam, or war. At first the invaders respected the who ran the government for them during the first few decades of occupation. came back to Alexandria and was able to restore monasteries and churches.

However, like the Romans, the Arabs were interested in the revenues of the country. were considered dhimmis, that is, “protected people,” in return for a payment of the poll tax in addition to the land tax. By 705 the monks had to pay the poll tax for the first time. In the following centuries, more financial burdens were imposed on the Copts. By the late ninth century, the did not represent the majority of Egypt’s population because of a combination of factors that led to their to Islam.