I can comment at length about the reasons for the end of Christianity in North Africa (so to speak), although I’m afraid I must delegate to others about the reasons for the survival of Christianity in Egypt. First off, I think /u/spoonfeedme makes a good point about the problems of homogenizing North Africa as entirely Christian in the years leading up to the Islamic conquests. There were certainly sizable populations of Christians there, especially on the coast, but farther inland it is difficult to tell how the Berbers (native North Africans) reacted to Christian missionaries. Some of them probably converted, some of them probably hybridized Christianity with their pre-existing beliefs, and some of them probably rejected Christian thought.

In the years following the Islamic conquests of the 7th century, we are left with records that document continued Christian presence in the region. One letter from Pope Gregory VII (r. 1073-1085) threatens the Christian community of Carthage with anathema if they do not repent for accusing their own bishop of certain crimes. Such a letter is indicative of tension within the Christian community, for Pope Gregory implies that the community sought the jurisdiction of an Islamic court over a Christian one for the crimes of the bishop. Other Arabic chronicles document the survival of North African Christianity into the 12th century. Ibn al-Athir mentions how, when the Normans seized the city of Mahdia in the 1140s, Muslims fled to the churches there. An inventory of the bishop of Mahdia further reveals that there was a measure of wealth into the middle of the 12th century.

However, the end to North African Christianity is traditionally found during the reign of the Almohads, an Islamic movement that swept through Morocco, al-Andalus, and Ifriqiya during the twelfth century. They expelled Christian populations during their invasions, as documented by a variety of sources. In particular, their expulsion of the Normans from Ifriqiya ended hundreds of years of continual Christian presence in the region. Granted, we only know as much as the sources tell us about these expulsions. We know very little about the fate of Christian communities outside of the African littoral. There undoubtedly remains some worthwhile archaeological work to be done on the topic, but it has not been completed at this time.

Although the Almohads drove out the majority, if not all, of “indigenous” Christian communities in North Africa, there remained Christians in the region who were there for business. In 1157 the Almohads made a treaty with Pisa that granted Pisan merchants certain commercial privileges in North African cities. The Almohads would continue to facilitate commerce with the Italian maritime cities throughout their time in power. In addition, the rulers of North Africa frequently employed Christian mercenaries in their fighting forces, which became a thorny issue for the Papacy during the 13th and 14th centuries. Finally, there were even priests who lived in North Africa who tended to the assortment of merchants and soldiers living there. Thus, although we might be able to date an end to indigenous Christianity to the Almohad conquests, certain Christian communities were able to establish themselves in the aftermath.

Hopefully that answers some of your questions. Sorry I couldn’t be of more help on the Egypt issue, though. The Copts remain a mystery to me!

Useful readings (French scholars have done much of the most significant work on this topic, which are understandably written in French):

Abulafia, David. “The Norman Kingdom of Africa and the Norman Expeditions to Majorca and the Muslim Mediterranean.” Anglo-Norman Studies 7 (1985): 26–49.

Abun-Nasr, Jamil. A History of the Maghrib in the Islamic Period. 3rd ed. New York: Cambridge University Press, 1987.

Brett, Michael. “Muslim Justice Under Infidel Rule: The Normans in Ifriqiya, 517-55H/1123-1160AD.” Cahiers de Tunisie 43 (1995): 325–68.

Brett, Michael and Elizabeth Fentress. The Berbers. Malden: Blackwell Publishing, 1997.

Constable, Remie. Housing the Stranger in the Mediterranean World: Lodging, Trade, and Travel in Late Antiquity and the Middle Ages. New York: Cambridge University Press, 2003.

De Mas Latrie, M.L. Traités de paix et de commerce et documents divers concernant Les relations des chrétiens avec les arabes de l’Afrique Septentrionale au moyen age. Paris: Henri Plon, 1866.

Handley, Mark. “Disputing the End of African Christianity.” In Vandals, Romans and Berbers: New Perspectives on Late Antique North Africa, edited by A.H. Merrills, 291–310. Burlington: Ashgate Publishing Limited, 2004.

Idris, H.R. La Berberie orientale sous les Zirides: Xe-XIIe siècles. Vol. 2. 2 vols. Limoges: A. Bontemps, 1962.

Jenkins, Philip. The Lost History of Christianity. HarperOne, 2009.

Valérian, Dominique. “La permanence du christianisme au Maghreb: l’apport problematique des sources latines.” In Islamisation et arabisation de l’Occident musulman (VIIe-XIIe siecle), 131–49. Paris: Publications de la Sorbonne, 2011.

Is it accurate to say that North Africa was almost entirely Christian? I know that the Vandals and then the Byzantines were definitely Christian, but what percentage of the indigenous population were?

Egypt is in Northern Africa. Why do you refer to them as separate entities?

Church in Egypt was very well established at the time Islam begun to spread. They was also did have differensies with Constantinopel about different dogmas and was supresed (Egypt was monofysits). In some ways egypt therefor did choose there overlord, mulsims, becouse of that they did tolarate there form of christianity. That is one reason for that christianity did survive.

In the entire christian world during monastaries was a big part of revitalize (and spread) the religion among both high and low. In egypt the monastarian moments did begun with desertfathers/mothers around year 300. The moment did live on and I have friends that have traveld to visit egyptian monastaries in the last decade. That did absolutly had part in helping the christian community to survive in Egypt till present day.

These two resons are both present prior to the muslim conquest and are present during the muslim reign. But I do not know if I have sources for how they did help the community under muslims.

Sources: Jonathan Hill; Zondervan Handbook to the History of Christianity [sorry, but I´m tired for the moment, I will hopefully extend sources more tomorrow]

Islam appealed to mostly the poor. Egypt, the levant, and Persian populations ended up preferring Muslim rule because, even with the dhimmi tax, those populations were still taxed less than the were under the Byzantines and Persians.

So in addition to that, it is forbidden for a Muslim to tax other Muslims. So a vast majority of converts converted for the tax break.

The rich, though, did not convert. Thier wealth persisted even until today in some cases (Coptic Christians in Egypt for example).

There were other more specific scenarios, but this was the most general reason.