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The Muslim conquest of Egypt by the Arabs took place between 639 and 646 AD and was overseen by the Rashidun Caliphate. It ended the centuries long period of Roman/Byzantine reign (beginning in 30 BC) over Egypt. Byzantine rule in the country had been shaken, as Egypt had been conquered and occupied for a decade by the Sassanid Empire in 618-629, before being recovered by the Byzantine emperor Heraclius. The Caliphate took advantage of the Byzantines' exhaustion and captured Egypt ten years after its reconquest by Heraclius.
During the mid-630s, Byzantium had already lost the Levant and its Ghassanid allies in Arabia to the Caliphate. The loss of the prosperous province of Egypt and the defeat of the Byzantine armies severely weakened the empire, resulting in further territorial losses in the centuries to come.
In December 639, 'Amr ibn al-'As left for Egypt with a force of 4,000 troops. Most of the soldiers belonged to the Arab tribe of 'Ak, but Al-Kindi mentioned that one third of the soldiers belonged to the Arab tribe of Ghafik. The Arab soldiers were also joined by some Roman and Persian converts to Islam. However, 'Umar, the Muslim caliph, reconsidered his orders to Amr and considered it foolhardy to expect to conquer such a large country as Egypt with a mere 4,000 soldiers. Accordingly, he wrote a letter to 'Amr ordering him to come back.
The messenger, 'Uqbah ibn 'Amr, caught up with Amr at Rafah, a little short of the Egyptian frontier. Guessing what might be in the letter, 'Amr ordered the army to quicken its pace. Turning to 'Uqbah, 'Amr said that he would receive the caliph's letter from him when the army had halted after the day's journey. 'Uqbah, unaware of the contents of the letter, agreed and marched along with the army. The army halted for the night at Shajratein, a little valley near the city of El Arish, which 'Amr knew to be beyond the Egyptian border. 'Amr then received and read 'Umar's letter and went on to consult his companions as to the course of action to be adopted. The unanimous view was that as they had received the letter on Egyptian soil, they had permission to proceed.
When 'Umar received the reply, he decided to watch further developments and to start concentrating fresh forces at Madinah that could be dispatched to Egypt as reinforcements. On Eid al-Adha, the Muslim army marched from Shajratein to El Arish, a small town lacking a garrison. The town put up no resistance, and the citizens offered allegiance on the usual terms. The Muslim soldiers celebrated the Eid festival there.
In of December 639 or early January 640, the Muslim army reached Pelusium, a garrison city considered to be the eastern gateway to Egypt at the time. The siege of the town dragged on for two months. In February 640, an assault group, led by the prominent Huzaifah ibn Wala, successfully captured the fort and city. Armanousa, the daughter of the Egyptian governor, Cyrus, who, after fiercely resisting the Muslims in Pelusium, fell into their hands but was sent to her father in the Babylon Fortress.
The losses incurred by the Muslim army were ameliorated by the number of Sinai Bedouins, who, taking the initiative, had joined them in conquering Egypt. The Bedouins belonged to the tribes of Rashidah and Lakhm.
The ease with which Pelusium fell to the Muslims and the lack of Byzantine reinforcements during the month-long siege is often attributed to the treachery of Cyrus, who was also the Monothelite/Monophysite Patriarch of Alexandria.
After the fall of Pelusium, the Muslims marched to Belbeis, 65 km (40 mi) from Memphis via desert roads, and besieged it. Belbeis was the first place in Egypt that the Byzantines showed some measure of resistance towards the Arabs. Two Christian monks, accompanied by Cyrus of Alexandria and the famous Roman general Aretion, came out to negotiate with 'Amr ibn al-'As. Aretion had been the Byzantine governor of Jerusalem and had fled to Egypt when the city fell to the Muslims. 'Amr gave them three options: convert to Islam, pay the jizya, or fight. They requested three days to reflect and then, according to al-Tabari, requested two extra days.
At the end of the five days, the two monks and the general decided to reject Islam and the jizya and fight the Muslims, thus disobeying Cyrus, who wanted to surrender and pay jizya. Cyrus left for the Babylon Fortress. The battle resulted in a Muslim victory during which Aretion was killed. 'Amr ibn al-'As subsequently attempted to convince the native Egyptians to aid the Arabs and surrender the city, based on the kinship between Egyptians and Arabs via Hagar. When the Egyptians refused, the siege resumed until the city fell around the end of March 640. Now, the Arabs were only one day away from the head of the Delta.
Amr had assumed that Egypt would be a pushover but was quickly proven wrong. Even at the outposts of Pelusium and Belbeis, the Muslims had met stiff resistance, with sieges of two and one months, respectively. As Babylon, near what is now Cairo, was a larger and more important city, resistance on a larger scale was expected. The Muslims arrived at Babylon some time in May 640.
Babylon was a fortified city, and the Romans had indeed prepared it for a siege. Outside the city, a ditch had been dug, and a large force was positioned in the area between the ditch and the city walls. The Muslims besieged the fort, a massive structure 18 m (59 ft) high with walls more than 2 metres (6.6 feet) thick and studded with numerous towers and bastions and a force of some 4,000 men. Early Muslim sources place the strength of the Byzantine force in Babylon at about six times the strength of the Muslim force. For the next two months, fighting remained inconclusive, with the Byzantines repulsing every Muslim assault.
Later the same month, 'Amr sent a detachment to raid the city of Fayoum. The Byzantines had anticipated that and so had strongly guarded the roads that led to the city and had fortified their garrison in the nearby town of Lahun. When the Muslims realised that Fayoum was too strong for them to take, they headed towards the Western Desert, where they looted all the cattle and animals that they could. They subsequently headed to Oxyrhynchus (Per-Medjed), which was defeated. The Arabs then returned to Lower Egypt down the River Nile.
In July, 'Amr wrote to 'Umar requesting reinforcements, but before the letter reached him, the caliph had already dispatched 4,000 men, mostly veterans of the Syrian campaigns, to bolster Amr's strength. Even with the reinforcements, 'Amr was unsuccessful and so, by August, 'Umar had assembled another 4,000-strong force, consisting of four columns, each of 1,000 elite men. Zubair ibn al-Awam, a renowned warrior and commander, veteran of the Battle of Yarmouk and once a part of Khalid ibn Walid's elite mobile guard, was appointed the supreme commander of the army.
'Umar had also offered Zubair the chief command and governorship of Egypt, but Zubair had declined. The column commanders included Miqdad ibn al-Aswad, Ubaidah ibn as-Samit and Kharijah ibn Huzaifah. The reinforcements arrived at Babylon sometime in September 640, bringing the total strength of the Muslim force to 12,000, still quite modest.
The Muslim army reached Heliopolis, 15 km (10 mi) from Babylon, in July 640. The city boasted the Sun Temple of the Pharaohs and grandiose monuments and learning institutions. There was the danger that forces from Heliopolis could attack the Muslims from the flank while they were engaged with the Roman army at Babylon.
There was a cavalry clash near the current neighbourhood of Abbaseya. The engagement was not decisive, but it resulted in the occupation of the fortress located between the current neighborhoods of Abdyn and Azbakeya. The defeated Byzantine soldiers retreated to either the Babylon Fortress or the fortress of Nikiû. Zubair and some of his handpicked soldiers scaled the Heliopolis city wall at an unguarded point and, after overpowering the guards, opened the gates for the army to enter the city. After the capture of Heliopolis, 'Amr and Zubair returned to Babylon.
When news of the Muslims' victory at Heliopolis reached Fayoum, its Byzantine garrison, under the command of Domentianus, evacuated the city during the night and fled to Abuit and then down the Nile to Nikiu without informing the people of Fayoum and Abuit that they were abandoning their cities to the enemy. When news reached 'Amr, he sent troops across the Nile to invade Fayoum and Abuit, capturing the entire province of Fayoum without any resistance.
The Byzantine garrison at Babylon had grown bolder than ever before and had begun to sally forth across the ditch but with little success. The stalemate was broken when the Muslim commanders devised an ingenious strategy, inflicting heavy casualties on the Byzantine forces by encircling them from three sides during one of their sallies. The Byzantines were able to retreat back to the fort, but were left too weak for any further offensive action, forcing them to negotiate. The Byzantine general, Theodorus, shifted his headquarters to the Isle of Rauda, and Cyrus of Alexandria, popularly known as Muqawqis in Muslim history, entered into fruitless negotiations with the Muslims.
Emissaries were also exchanged between Theodorus and 'Amr, leading to 'Amr meeting Theodorus in person. Then, with negotiations stalled, during the night of 20 December, a company of handpicked warriors, led by Zubair, managed to scale the wall, kill the guards, and open the gates for the Muslim army to enter. The city was captured by the Muslims the following morning with tactics similar to those that had been used by Khalid ibn Walid at Damascus. However, Theodorus and his army managed to slip away to the island of Rauda during the night.
On 22 December, Cyrus of Alexandria entered a treaty with the Muslims, recognizing Muslim sovereignty over the whole of Egypt and effectively over Thebaid, and agreeing to pay Jizya at the rate of 2 diners per male adult. The treaty was subject to the approval of the emperor Heraclius, but Cyrus stipulated that even if the emperor repudiated the treaty, he and the Copts, of whom he was the High Priest, would honour its terms. Cyrus asked Heraclius to ratify the treaty and offered an argument in support. 'Amr submitted a detailed report to Umar recommending ratification. He desired that as soon as the reactions of Heraclius were known, he should be informed so that further necessary instructions could be issued promptly.
Heraclius rejected the treaty, stripping Cyrus of the viceroyship although he remained head of the Coptic Church. Heraclius sent strict orders to the commander-in-chief of the Byzantine forces in Egypt that the Muslims should be driven out of Egypt. Cyrus, in reporting Heraclius' response to 'Amr, reassured him that the Copts would honor the treaty regardless. It is recorded that Cyrus requested three favours from the Muslims:
As the Copts were native Egyptians, the treaty provided a strategic advantage to the Muslims. 'Umar, upon learning of these developments, made preparations for a pre-emptive strike against the Byzantines in Alexandria.
The Byzantine commanders, knowing full well that the Muslims' next target was Alexandria, set out to repel the Muslims through continued sallies from the fort or, at least, to exhaust them and erode their morale in a campaign of attrition. In February 641, 'Amr set off for Alexandria from Babylon with his army, encountering defending regiments all along the route. On the third day of their march the Muslims' advance guard encountered a Byzantine detachment at Tarnut on the west bank of the Nile. The Byzantines failed to inflict heavy losses but were able to delay the advance by a full day. The Muslim commanders decided to halt the main army at Tarnut and send an advance guard of cavalry forward to clear the path.
Now 30 km (19 mi) from Tarnut, the Byzantine detachment that had withdrawn from Tarnut the day before joined another that was already at Shareek, and both attacked and routed the Muslim cavalry. The next day, before the Byzantines could annihilate the Muslim advance guard completely, the main Muslim army arrived, prompting the Byzantines to withdraw. The following day, the whole army marched forward without an advance guard. The Muslims reached Sulteis, where they encountered another Byzantine detachment. Hard fighting followed, but the Byzantine resistance soon broke down and they withdrew to Alexandria.
The Muslims halted at Sulteis for a day, still two days' march from Alexandria. After another day's march, the Muslim forces arrived at Kirayun, 20 km (12 mi) from Alexandria. There, the Muslim advance to Alexandria was blocked by a Byzantine force about 20,000 strong. The resulting action remained indecisive for ten days. However, on the tenth day, the Muslims launched a vigorous assault, forcing the defeated Byzantines to retreat to Alexandria. With the way to Alexandria clear, the Muslims reached the capital's outskirts in March.
The Muslims laid siege to Alexandria in March 641. The city was heavily fortified and provisioned: there were walls within walls and forts within forts. The city also had direct access to the sea by which men and supplies from Constantinople could come at any time.
As 'Amr surveyed the military situation, he felt that the conquest of Alexandria would be difficult. The Byzantines had high stakes in Alexandria and were determined to offer stiff resistance to the Muslims. They mounted catapults on the walls of the city, and the engines effectively pounded the Muslims with boulders, prompting 'Amr to withdraw out of range. The ensuing battle see-sawed: when the Muslims approached the city, they were pelted with missiles, and, when the Byzantines sallied from the fort, they were invariably beaten back by the Muslims.
It is said[by whom?] that Heraclius, the Byzantine emperor, collected a large army at Constantinople, intending to lead it personally to Alexandria. However, before he could finalize the arrangements, he died. The troops mustered at Constantinople dispersed, and no help came to Alexandria, which further demoralied the defenders. The siege dragged on for six months, and in Madinah, 'Umar, got impatient. In a letter addressed to 'Amr, the caliph, concerned at the inordinate delay, appointed 'Ubaidah as field commander to assault the fort. 'Ubaidah's assault was successful, and Alexandria was captured by the Muslims in September. Thousands of Byzantine soldiers were killed or taken captive, and others managed to flee to Constantinople on ships that had been anchored in the port. Some wealthy traders also left.
On behalf of the Egyptians, Cyrus of Alexandria sued for peace, and his request was granted. After the conquest of Egypt, 'Amr is reported[by whom?] to have written to 'Umar, "We have conquered Alexandria. In this city there are 4,000 palaces, 400 places of entertainment, and untold wealth."
On the twentieth of Maskaram (approximately September 18 according to the Julian calendar), the Byzantine general, Theodorus, and all of his troops proceeded to the island of Cyprus, abandoning Alexandria to 'Amr. The conquest represented a huge loss of food and money to Byzantium and, coupled with the conquest of Syria and the later invasion of the Exarchate of Africa, meant that the Mediterranean, long referred to as the "Roman lake", was now contested between the Muslim Caliphate and the Byzantine Empire. The latter, although sorely tested, would be able to hold on to Anatolia, while the walls of Constantinople would withstand two great Muslim sieges, saving the Byzantines from the fate of the Persian Empire.
In the summer of 642, 'Amr ibn al-'As sent an expedition to the Christian kingdom of Nubia, which bordered Egypt to the south, under the command of his cousin 'Uqbah ibn Nafi as a pre-emptive raid to announce the arrival of new rulers in Egypt. 'Uqbah ibn Nafi, who later made a great name for himself as the conqueror of Africa and led his horse to the Atlantic, had an unhappy experience in Nubia. No pitched battle was fought, but there were only skirmishes and haphazard engagements, the type of warfare in which the Nubians excelled. They were skilful archers and subjected the Muslims to a merciless barrage of arrows, resulting in 250 Muslims losing their eyes in the engagement.
The Nubian cavalry displayed remarkable speed, even more so than the Muslim cavalry. The Nubians would strike hard and then vanish before the Muslims could recover and counterattack. The hit-and-run raids took their toll on the Muslim expedition. 'Uqbah reported that to 'Amr, who ordered 'Uqbah to withdraw from Nubia, terminating the expedition.
After the expedition to Nubia, 'Amr opted to secure the western borders of Egypt and clear the regions of Cyrenaica, Tripolitania and Fezzan of Byzantine influence. In September 642, 'Amr led his troops west. After one month of marching the Muslim forces reached the cities of the Pentapolis. From Burqa, he sent 'Uqbah bin Nafi at the head of a column to undertake a campaign against Fezzan, in present-day northwestern Libya. 'Uqbah marched to Zaweela, the capital; the entire district then submitted to the Muslims without resistance. 'Uqbah then returned to Burqa. Soon after the Muslim army marched westward from there, arriving at Tripoli in the spring of 643. The city fell after a siege of one month. From there, 'Amr sent a detachment to Sabratha, 65 kilometres (40 mi) away. The city put up feeble resistance, and soon surrendered and agreed to pay Jizya. From Tripoli, 'Amr is reported[according to whom?] to have reported to the caliph, "We have conquered Burqa, Tripoli and Sabratha. The way to the west is clear, and if the Commander of the Faithful wishes to conquer more lands, we could do so with the grace of God."
'Umar, whose armies were already engaged in conquering the Sassanid Empire, did not want to commit his forces further in North Africa while Muslim rule in Egypt was still insecure. The caliph accordingly ordered 'Amr to consolidate the Muslims' position in Egypt and that there should be no further campaigning. 'Amr obeyed, abandoning Tripoli and Burqa and returning to Fustat towards the close of 643.
Those who refused to convert to Islam were taxed in the form of money and food for the occupying troops, and in exchange, the taxpayers were excused from military service and left free in the observance of their religion and the administration of their affairs. The system was a new institution, a religious mandate, but carried over from previous poll tax systems in the ancient Middle East. Indeed, the Egyptians had been subject to it, as non-Romans, during Roman rule before the adoption of Christianity by the Roman state. Then, all non-Christian subjects of the Roman Empire had to pay it, including non-Christian Egyptians. The Persians also had a similar poll tax system.
John of Nikiu a Coptic bishop wrote a Chronicle which provides one of the few non-Muslim accounts of the conquest written by a native of Egypt who was also a near contemporary of the events. He writes of Muslim rule: "And the yoke they laid on the Egyptians was heavier than the yoke which had been laid on Israel by Pharaoh". Regarding taxation he writes that after the conquest taxes on the native Christians were increased "to the extent of twenty-two batr of gold till all the people hid themselves owing to the greatness of the tribulation, and could not find the wherewithal to pay."  Writing particularly as regards the taxation of the people of Alexandria, he notes:
And none could recount the mourning and lamentation which took place in that city: they even gave their children in exchange for the great sums which they had to pay monthly. And they had none to help them, and God destroyed their hopes, and delivered the Christians into the hands of their enemies.
Muslims gained control over Egypt by a variety of factors, including internal Byzantine politics, religious zeal and the difficulty of maintaining a large empire. The Byzantines attempted to regain Alexandria, but it was retaken by 'Amr in 646. In 654 an invasion fleet sent by Constans II was repelled. No serious effort was then made by the Byzantines to regain possession of Egypt.
In The Great Arab Conquests, Hugh Kennedy writes that Cyrus, the Roman governor, had exiled the Coptic patriarch, Benjamin. When 'Amr occupied Alexandria, a Coptic nobleman (duqs) called Sanutius persuaded him to send out a proclamation of safe conduct for Benjamin and an invitation to return to Alexandria. When Benjamin arrived, after 13 years in hiding, Amr treated him with respect. Benjamin was then instructed by the governor to resume control over the Coptic Church. He arranged for the restoration of the monasteries in the Wadi Natrun, which had been ruined by the Chalcedonean Christians; four of them still survive as functioning monasteries.
On Benjamin's return, the Egyptian population also worked with him. Kennedy wrote, "The pious biographer of Coptic patriarch Benjamin presents us with the striking image of the patriarch prayed for the success of the Muslim commander Amr against the Christians of the Cyrenaica. Benjamin survived for almost twenty years after the fall of Egypt to the Muslims, dying of full years and honour in 661. His body was laid to rest in the monastery of St Macarius, where he is still venerated as a saint. There can be no doubt that he played a major role in the survival of the Coptic Church". Benjamin also prayed for 'Amr when he attempted to take Libya.
Kennedy also wrote, "Even more striking is the verdict of John of Nikiu. John was no admirer of Muslim government and was fierce in his denunciation, but he says of Amr: 'He extracted the taxes which had been determined upon but he took none of the property of the churches, and he committed no act of spoliation or plunder, and he preserved them throughout all his days.... Of all the early Muslim conquests, that of Egypt was the swiftest and most complete. Within a space of two years the country had come entirely under Arab rule. Even more remarkably, it has remained under Muslim rule ever since. Seldom in history can so massive a political change have happened so swiftly and been so long lasting."
Uqba ibn Nafi then used Egypt as a launch pad to move across North Africa, all the way to the Atlantic Ocean. Kennedy wrote that when Uqba reached the Atlantic, he is said to have ridden his horse into the sea until the water was below his chest, and then shouted, 'O Lord, if the sea did not stop me, I would go through lands like Alexander the Great, defending your faith'. Kennedy writes further that the image of a warrior whose conquest in the name of God was stopped only by the ocean remains important in the history of the conquests.
During the Egyptian campaign, Alexandria was the capital of Egypt. When Alexandria was captured by the Muslims, the houses vacated by the Byzantines were occupied by the Muslims, who were impressed and attracted by Alexandria, "the queen of cities". 'Amr wanted Alexandria to remain the capital of Muslim Egypt. He wrote to 'Umar to propose that but 'Umar refused on the basis that Alexandria was a maritime city, and there would always be a danger that the Byzantine Navy would attack. He suggested instead for the capital would be established at a central location further inland, where no mass of water separated it from Arabia. The treaty with Cyrus of Alexandria was followed, and the wealth of the Egyptians in Alexandria was spared and that of Romans and Greeks was taken as booty. Greek citizens were given a choice: return to Greek territories safely without their wealth or stay in Alexandria and pay Jizya. Some chose to stay, and others went to Byzantine lands.
'Amr next proceeded to choose a suitable site for the capital of Egypt, eventually settling on the site where he had pitched his tent at the time of the battle of Babylon, about 400 m (500 yd) northeast of the fort. It is reported that after the battle was over and the army was about to march to Alexandria, the men began to pull down the tent and pack it for the journey, and it was found that a dove had nested on top of the tent and laid eggs. 'Amr ordered that the tent be left standing where it was, where it remained after the army departed. 'Amr took the unusual episode as a sign from Heaven and decided "where the dove laid its nest, let the people build their city".
As 'Amr's tent was to be the focal point of the city, the city was called Fustat, meaning in Arabic "the tent". The first structure to be built was the mosque that later became famous as Mosque of 'Amr ibn al-'As. In the course of time, Fustat extended to include the old town of Babylon to the west, becoming the bustling commercial centre of Egypt.
To consolidate his rule in Egypt, 'Umar imposed the jizya on Egyptians. During later Umayyad rule, higher taxes would be levied. With 'Umar's permission, 'Amr decided to build a canal to join the Nile with the Red Sea to open new markets for Egyptian merchants and an easy route to Arabia and Iraq. The project was presented to 'Umar, who approved it. A canal was dug and, within a few months, was opened for merchants. It was named "Nahar Amir ul-Mu'mineen" (the canal of the Commander of the Faithful), after 'Umar's title.
Amr proposed to dig another canal joining the Red Sea and the Mediterranean Sea, but Umar rejected the plan on the basis that it would open a way for the Byzantine Navy to enter the Red Sea and pose a threat to Medina itself. The plan would not come to fruition until the Suez Canal was completed 1300 years later. Each year, the caliph earmarked a large amount of jizya, to be used on the building and repairing of canals and bridges. The Arabs remained in control of the country from this point until 1250, when it fell under the control of the Mamluks.