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Israeli period

On 7 June 1967, during the Six-Day War, Israeli forces advanced beyond the 1949 Armistice Agreement Line into West Bank territories, taking control of the Old City of Jerusalem, inclusive of the Temple Mount.

The Chief Rabbi of the Israeli Defense Forces, Shlomo Goren, led the soldiers in religious celebrations on the Temple Mount and at the Western Wall. The Israeli Chief Rabbinate also declared a religious holiday on the anniversary, called " Yom Yerushalayim " (Jerusalem Day), which became a national holiday to commemorate the reunification of Jerusalem. Many saw the capture of Jerusalem and the Temple Mount as a miraculous liberation of biblical-messianic proportions. A few days after the war over 200,000 Jews flocked to the Western Wall in the first mass Jewish pilgrimage near the Mount since the destruction of the Temple in 70 CE. Islamic authorities did not disturb Goren when he went to pray on the Mount until, on the Ninth Day of Av, he brought 50 followers and introduced both a shofar, and a portable ark to pray, an innovation which alarmed the Waqf authorities and led to a deterioration of relations between the Muslim authorities and the Israeli government.

In June 1969, an Australian set fire to the Jami'a al-Aqsa. On April 11, 1982, a Jew hid in the Dome of the Rock and sprayed gunfire, killing 2 Palestinians and wounding 44; in 1974, 1977 and 1983 groups led by Yoel Lerner conspired to blow up both the Dome of the Rock and al-Aqsa. On 26 January 1984 Waqf guards detected members of B'nei Yehuda, a messianic cult of former gangsters turned mystics based in Lifta, trying to infiltrate the area to blow it up.

On 15 January 1988, during the First Intifada, Israeli troops fired rubber bullets and tear gas at protesters outside the mosque, wounding 40 worshipers.

On October 8, 1990, Israeli forces patrolling the site blocked worshippers from reaching it. A tear gas canister was set off among the female worshippers, which caused events to escalate. On 12 October 1990 Palestinian Muslims protested violently the intention of some extremist Jews to lay a cornerstone on the site for a New Temple as a prelude to the destruction of the Muslim mosques. The attempt was blocked by Israeli authorities but demonstrators were widely reported as having stoned Jews at the Western Wall. According to Palestinian historian Rashid Khalidi, investigative journalism has shown this allegation to be false. Rocks were eventually thrown, while security forces fired rounds that killed 21 people and injuring 150 more. An Israeli inquiry found Israeli forces at fault, but it also concluded that charges could not be brought against any particular individuals.

On 8 October 1990, 22 Palestinians were killed and over 100 others injured by Israeli Border Police during protests that were triggered by the announcement of the Temple Mount Faithful, a group of religious Jews, that they were going to lay the cornerstone of the Third Temple. Between 1992 and 1994, the Jordanian government undertook the unprecedented step of gilding the dome of the Dome of the Rock, covering it with 5000 gold plates, and restoring and reinforcing the structure. Saladin's minbar was also reconstructed. The project was paid for by King Hussein personally, at a cost of $8 million. The Temple Mount remains, under the terms of the 1994 Israel–Jordan peace treaty, under Jordanian custodianship. In December 1997, Israeli security services preempted an attempt by Jewish extremists to throw a pig's head wrapped in the pages of the Quran into the area, in order to spark a riot and embarrass the government.

On 28 September 2000, then-opposition leader of Israel Ariel Sharon and members of the Likud Party, along with 1,000 armed guards, visited the al-Aqsa compound. The visit was seen as a provocative gesture by many Palestinians, who gathered around the site. After Sharon and the Likud Party members left, a demonstration erupted and Palestinians on the grounds of the Haram al-Sharif began throwing stones and other projectiles at Israeli riot police. Police fired tear gas and rubber bullets at the crowd, injuring 24 people. The visit sparked a five-year uprising by the Palestinians, commonly referred to as the al-Aqsa Intifada, though some commentators, citing subsequent speeches by Palestinian Authority officials, particularly Imad Falouji and Yasar Arafat, claim that the Intifada had been planned months in advance, as early as July upon Arafat's return from Camp David talks in the United States. On 29 September, the Israeli government deployed 2,000 riot police to the mosque. When a group of Palestinians left the mosque after Friday prayers (Jumu'ah,) they hurled stones at the police. The police then stormed the mosque compound, firing both live ammunition and rubber bullets at the group of Palestinians, killing four and wounding about 200.

On 3 January 2023, Israeli Minister of National Security Itamar Ben-Gvir visited the Temple Mount in Jerusalem, sparking protests by Palestinians and the condemnation of several Arab countries.