Excavations in Malha revealed Intermediate Bronze Age domestic structures. A dig in the Rephaim Valley carried out by the Israel Antiquities Authority in the region of the Malha shopping mall and Biblical Zoo uncovered a village dating back to the Middle Bronze Age II B. Beneath this, remains of an earlier village were found from the Early Bronze Age IV. According to the archaeologists who excavated there in 1987–1990, Malha is believed to be the site of Manahat, a Canaanite town on the northern border of the Tribe of Judah. Remains of the village have been preserved at the Biblical Zoo.
Ottoman era
In the 1596 tax records al-Maliha,, was part of the Ottoman Empire, nahiya of Jerusalem under the Liwa of Jerusalem. It had a population of 52 Muslim households, an estimated 286 persons. The villagers paid a fixed tax rate of 33,3% on wheat, barley, and olive and fruit trees, goats and beehives; a total of 8,700 akçe. 1/3 of the revenue went to a waqf. In 1838 it was noted by Edward Robinson as el Malihah, a Muslim village, part of the Beni Hasan district. An Ottoman village list from about 1870 showed Malha with a population of 340, in 75 houses, though the population count included men, only. In 1883, the PEF's Survey of Western Palestine described the village as being of moderate size, standing high on a flat ridge. To the south was Ayn Yalu. In 1896 the population of Malha was estimated to be about 600 persons.
British Mandate era
In the 1922 census of Palestine conducted by the British Mandate authorities, Malhah had a population 1,038, all Muslims, increasing in the 1931 census to 1,410; 1,402 Muslims and 8 Christians, in a total of 299 houses. In the 1945 statistics the population of Malha was 1,940; 1,930 Muslims and 10 Christians, and the total land area was 6,828 dunams, according to an official land and population survey. Of the land, a total of 2,618 dunams were plantations and irrigable land and 1,259 were for cereals, while a total of 328 dunams were built-up land.
1948
In the 1948 Arab-Israeli War, the village of al-Maliha, with a population of 2,250, was occupied as part of the battle for south Jerusalem. In the early part of the war, Al-Maliha, along with al-Qastal, Sur Baher and Deir Yassin, signed non-aggression pacts with the Haganah. On April 12, 1948, in the wake of the Deir Yassin Massacre, villagers from al Maliha, Qaluniya and Beit Iksa began to flee in panic. The Irgun attacked Malha in early morning hours of July 14, 1948. Several hours later, the Palestinian Arabs launched a counter-attack and seized one of the fortified positions. When Irgun reinforcements arrived, the Palestinians retreated and Malha was in Jewish control, but 17 Irgun fighters were killed and many wounded. The Arab inhabitants fled to Bethlehem, which remained under Jordanian control. The depopulated homes were occupied by Jewish refugees from Middle Eastern countries, mainly Iraq. Some of the land in Malha had been purchased before the establishment of the state by the Valero family, a family of Sephardi Jews that owned large amounts of property in Jerusalem and environs.
After 1948
The first Palestinian fedayeen raid in Israel took place in November 1951 in Malha when a woman, Leah Festinger, was killed by infiltrators from Shuafat, at the time part of Jordan.
