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'Umar decided to return to the aborted conquest of Israel. What was originally a mission of mercy became a mission of conquest. The Muslim army was in three divisions of 5000 men each, the commanders being 'Amr ibn al-'As, Shurahbil ibn Hasana, and Yezid. To each of these divisions one of the districts of Syria-Palestine was assigned as its field of operations. 'Amr and his Jewish troops were to make for Ayla, at the head of the Gulf of Aqaba, and thence invade southern Syria or Israel. Shurahbil and his Sadducean troops were to make first for Tebuk, whence the latter was to invade central Syria, while Yezid and his formerly Christian troops pushed on towards Damascus. Mu'awiya, the future Khalif, bore the standard of his brother Yezid. Hebron (with its tombs of the Jewish patriarchs) fell to 'Amr, but a greater battle awaited.

In 635, Battle of Yarmuk occurred. Convinced that the Rome was at war with the Jews, Emperor Heraclius decreed forced baptism on North African Jewish communities. Heraclius started organizing an international force, as many as 70,000 troops. The Muslims reached Damascus, but were forced to withdraw to Yarmuk. Heraclius ordered that his troops were to persue the Muslims, stipulating that they were not to engage them in war, but rather to keep on the alert until he could assemble his other troops and send them to help. Now the Byzantines reached the Jordan and crossed into Arabia [trans-Jordan]. Leaving their campsite on the riverbank, the Byzantines went on foot to attack the Muslims' camp. The Muslims, however, had placed part of their army in ambuscades here and there, lodging the multitude in dwellings around the camp. Then they drove in herds of camels which they penned around the camp and the tents, tying them at the foot with rope. Such was the fortification of their camp. The beasts were fatigued from the journey, and so the Byzantines were able to cut through the camp fortification, and started to kill the Muslims. But suddenly the men in the ambuscades sprung from their places and fell upon them. The Byzantine troops turned in flight before them. There was great anxiety caused by the heat of the sun and the enemy's sword was upon them. All the generals fell and perished. More than 2,000 men were slain. A few survivors fled to a place of refuge.

After defeating the Byzantines, they marched onward to capture Damascus. In 636 CE Gaza was conquered. 'Umar visited Syria to begin to develop governmental policies. In 637 CE, Caesarea was under siege for seven months until a Jew named Joseph led the Moslem attackers through a tunnel to capture the city. Later that year Damascus fell.

After the capture of Damascus, the Muslims crossed the Jordan and encamped at Jericho. Then dread of them came over the inhabitants of the country, and all of them submitted. That night the chief citizens of Jerusalem took the "Cross of the Lord" and all the vessels of the churches, and fled with them by boat to the palace at Constantinople. The Jerusalemites requested an oath from the Arabs and then submitted, but only if the Khalif would come in person to confirm the treaty.

'Umar arrived from Damascus. After finalizing the Pact of 'Umar with the leaders of Jerusalem, he requested to see the Temple mount. When 'Umar reached the old ruined gates of the Temple he was horrified to see the filth, "which was then all about the holy sanctuary, had settled on the steps of the gates so that it even came out into the streets in which the gate opened, and it had accumulated so greatly as almost to reach up the ceiling of the gateway." The only way to get up to the platform was to crawl on hands and knees. Sophronius went first and the Muslims struggled up behind. When they arrived at the top, the Muslims gazed appalled at the vast and desolate expanse of Herod's platform, still covered with piles of fallen masonry and garbage. The shock of this sad encounter with the holy place whose fame had reached them in far-off Arabia was never forgotten: Muslims claimed that they called Anastasis al-qumamah, "the Dungheap," in retaliation for the impious of the Christians on the Temple Mount.

'Umar does not seem to have spent any time on this occasion examining the Sakhrah rock, which would later play such an important part in Islam in the future – but rather concentrated on cleaning the Temple mount of filth. Once he had taken stock of the situation, he threw handfuls of dung and rubble into his cloak and then hurled it over the city wall into the Valley of Hinnom. Immediately his followers did the same.

When 'Amr and his Jewish soldiers arrived in Jerusalem, they planned to [re]build the Temple. At the time they enjoyed full support from the Sadducean Muslims (Hagarenes). Locating the place called the holy of holies; they constructed a wooden building with a pedestal, to serve as their place of prayer. But the Christians objected, and the Christian converts to Islam (Ishmaelites) envied the Jews. They expelled the Jews from that place, and named used the same building their own place of prayer. The Jews built another temple for their worship, elsewhere, on the southern side of the Temple Mount. This segmentation of Jerusalem along religious lines seemed to be part of 'Umar's policy towards Jerusalem. It was during this early Muslim period that Jerusalem was divided into different quarters for each religious community.

The area on the Temple Mount which now contains the Qubbat Al-Sakhrah, Dome of the Rock was never venerated by Christians during all the centuries of Byzantine rule. When the Jews tried to build a house of prayer there, the Christian converts to Islam "out of jealousy" claimed it for their own. Its use as Christian-Islamic shrine from that point on is seen in the content of the inscriptions on the Qubbat Al-Sakhrah, Dome of the Rock, which are almost exclusively written to Christians. Benjamin of Tudela, writing during the crusades, says "our ancient Temple, [is] now called Templum Domini. Upon the site of the sanctuary Omar ben al Khatab [actually 'Abd al-Malik] erected an edifice with a very large and magnificent cupola, into which the Gentiles do not bring any image or effigy, but they merely come there to pray." The Qubbat Al-Sakhrah, Dome of the Rock was never made properly a mosque. It remained a shrine for Muslims and non-Muslims (particularly Christians) to enter and pray.