The Early Islamic Period (640-969) Under the first Khalif of Islam Abu Bakr As-Siddiq, the Prophet Muhammad's closest companion, the Muslim armies vanquished the Byzantines in AD636. They advanced toward Egypt under the command of Amr Ibn Al-As, one of the companions of the Prophet. The Muslims laid seige to Babylon-in-Egypt which surrendered. They then took Heliopolis and in AD642 the Byzantine imperial capital of Alexandria.

Amr Ibn Al-As established Fustat north of Babylon-in-Egypt as his military headquarters and seat of government and the Egyptians swiftly embraced the new religion of Islam. Egypt became part of an expanding empire that was soon to stretch from Spain to Central Asia. The Umayyad Dynasty ruled Egypt from Damascus until the Abbassids took control of the Khalifate and shifted the political capital of Islam to Baghdad. Ahmad Ibn Tulun who had been sent by the Abbassid Khalif Al-Mu'taz to govern Egypt in AD868, declared Egypt an independent state and successfully defended his new domain against the Abbassid armies sent to unseat him. His dynasty ruled Egypt for 37 years.

Ibn Tulun built Al-Qitai, a new capital centred around a vast central mosque, the courtyard of which could accommodate his entire army and their horses. But Tulunid rule was quickly ended by the Abbassids, who retained direct control over Egypt until Mohammed Ibn Tughj was appointed governor over the province and granted the title Ikhshid, allowing him to rule independently of khalifal controls. The Ikhshidid Dynasty ruled from AD935-969 when Egypt was invaded by Shi'a Fatimid armies from Tunisia.