The frequent incursions into Syria from the Egyptian side and the harassment to which the sea-board was subjected by the Romans, led the Caliph, after some hesitation, to authorize an expedition into the land of the Pharaohs. Amr Ibn Al-Aas started with only 4,000 men. The success of Amr was due to the bad condition of Egypt in the last part of the Roman reign: such was their oppression in collecting the various taxes that the people were groaning and craving for a better life in the change of rules. The taxes levied numbered more than twenty, the heaviest of which were the wheat tax, the capitation and the land tax. What made matters worse were the religious disputes accompanied by persecution, all of which caused the ruination of the country. There was a bitter hostility between the national Monophysite of "Jacobite", and the official "Chalcedonian" (which the curators of Constantinople supported in Egypt). Cruelly persecuted, the Jacobites looked forward to a change that was to bestow tolerance upon them. Moreover, the standing army was powerless against any foreign invasion. And these conditions combined made the Egyptians welcome the new conquerors.
On crossing the eastern frontiers of Egypt, Amr with his 4,000-men-army, almost all horsemen, armed with lances, swords and bows, marched along the caravan route along the coast of Sinai facing no difficulty. The first opposition the Arabs met was at Pelusuim (el Farma) where the Roman garrison held out for a month. Again, Amr besieged Belbeis (some thirty miles from Misr) for a month before it surrendered. On his way to the fortress of Babylon, he defeated scanty grouping of the Romans and the rest retreated to a fortress where they could defend themselves for some time. This ancient castle still stands (at least in part) and is known as Kasr-esh-Shema. It was built by Trajan on the site of a Persian fort, and had been fortified by the Romans not long before the Arab invasion.
Before approaching the castle, Amr occupied "Umm Duneyn" (Ezbekiya), a village lying a little to the north of the fortress. Its possession gave him the command of plenty of boats, and he sent bands of his Arabs up the river to invade the Faiyum Oasis and other parts of Upper Egypt. The Arabs counted on the aid of at least the neutrality of the native Copts, of whose hostility to the Romans Amr had become well aware during his earliest visit to Egypt.
About the middle of June 640, a big reinforcement of 12,000 men under Ez-Zubair Ibn El Awwam, accompanied by several of the companions of the Prophet was sent at Amr's request. He had taken up a position at Heliopolis (on, Ain-Shams), some miles to the north of Babylon. In July 640, the Romans were routed with much slaughter at Heliopolis and fled to Babylon.
The Arabs besieged the fortress for eight months and its garrison at last capitulated on April 641.
Before the battle of Heliopolis, El Mukawkis "Cyrus" (the governor of Egypt and the powerful patriarch of Alexandria), accompanied by others, opened negotiations with the Arabs with a view to peace. The Arabs offered: conversion to Islam, or the payment of a poll-tax, or war to the knife. The negotiators were willing to submit to the poll-tax, but the Roman garrison utterly refused. When the garrison found the situation critical, they renewed the negotiation and submitted to the poll-tax, provided that the fortress should be left in their hands until Heraclius gave his final decision. Heraclius utterly repudiated this agreement, summoned Cyrus to Constantinople to account for his conduct, and reproached and disgraced him Heraclius' death precluded any hope of relief from Constantinople. Accordingly, the weary garrison of Babylon submitted in April 641. When the fortress of Babylon was taken, the Arab general marched north towards Alexandria along the Rosetta branch and defeated all the Roman troops he met on his way. On reaching Alexandria, he besieged it then left an army surrounding it and went with his troops to conquer other parts. He passed through Sakha and Athreeb in the Delta and continued his march in Upper Egypt as far as Thebes. He then came back to Babylon where he found Cyrus had returned armed with full powers to conclude a treaty which was finally signed in November 641, the chief articles of which were:
1) Those who held their own creed were to pay the poll-tax.
2) It was agreed that the Alexandrians should pay a monthly tribute, and deliver up 150 soldiers and 50 civilians as hostages.
3) The Muslims should not interfere with the churches and affairs of the Christians.
5) The Muslims should hold aloof from Alexandria for 11 months during which the Roman army would leave the city and embark. And they embarked in September 642.
The Arabs took another year to complete their conquest since they met serious resistance in some towns and provinces. Amr extended his conquest to Libya, because it had been ceded to Egypt during the last period of the Byzantine rule. So, he marched on and captured Cyranaica and Tripoli. His soldiers went southward to the northern frontiers of the Sudan.
The whole of Egypt, up to the borders of the Sudan on the south and Libya on the west, became subject to Muslim domination. Measures were taken to improve the conditions of the peasantry. The land was left in the hands of the cultivators; the old irrigation works were restored and the ancient canal connecting the Mediterranean Sea with the Red Sea was cleared out. The Egyptian Christians (who are called the Copts) were treated with marked favor in consequence of their good will towards the Muslims. Taxation was regulated upon a fixed and moderate scale, and trade was fostered by light customs dues.