The First Fitna, a major early Islamic civil war, led to significant changes in Egypt's governance. During this period, Caliph Ali appointed Muhammad ibn Abi Bakr as Egypt's governor. However, Amr ibn al-As, supporting the Umayyads, defeated Ibn Abi Bakr in 658 and governed Egypt until his death in 664. Under the Umayyads, pro-Umayyad partisans like Maslama ibn Mukhallad al-Ansari continued to govern Egypt until the Second Fitna. During this conflict, the Kharijite-supported Zubayrid regime, unpopular among local Arabs, was established. Umayyad Caliph Marwan I invaded Egypt in 684, reinstating Umayyad control and appointing his son, Abd al-Aziz, as governor, who ruled effectively as a viceroy for 20 years.^[82]

Under the Umayyads, governors like Abd al-Malik ibn Rifa'a al-Fahmi and Ayyub ibn Sharhabil, chosen from the local military elite (jund), implemented policies that increased pressure on the Copts and initiated Islamization.^[83] This led to several Coptic revolts due to heightened taxation, the most notable being in 725. Arabic became the official government language in 706, contributing to the formation of Egyptian Arabic. The Umayyad period ended with further revolts in 739 and 750.

During the Abbasid period, Egypt experienced new taxations and further Coptic revolts. Caliph al-Mu'tasim's decision in 834 to centralize power and financial control led to significant changes, including the replacement of local Arab troops with Turkish soldiers. The 9th century saw the Muslim population surpassing the Coptic Christians, with Arabization and Islamization processes intensifying. The "Anarchy at Samarra" in the Abbasid heartland facilitated the rise of Alid revolutionary movements in Egypt.^[84]

The Tulunid period began in 868 when Ahmad ibn Tulun was appointed as the governor, marking a shift towards Egypt's political independence. Despite internal power struggles, Ibn Tulun established a de facto independent rule, accumulating significant wealth and extending influence into the Levant. His successors, however, faced internal strife and external threats, leading to the Abbasid reconquest of Egypt in 905.^[85]

Post-Tulunid Egypt saw continued conflicts and the rise of influential figures like the Turkish commander Muhammad ibn Tughj al-Ikhshid. His death in 946 led to the peaceful succession of his son Unujur and the subsequent rule of Kafur. However, the Fatimid conquest in 969 ended this period, ushering in a new era of Egyptian history.^[86]