The village may be the site of the Battle of Beth Zechariah between the JewishMaccabeans and SelucidGreek forces during the Maccabean revolt against the Seleucid Empire, in the year 162 BCE. However, other sources place the battle at Zekharia/Az-Zakariyya in modern Israel. Three rock-cut burial caves, dating to the 1st century BCE have been excavated, and pottery fragments from the 1st century BCE were found. In the Byzantine period an important church was located here, which appears on the Madaba map. Since then a mosque, going by the name Nabi-Zakariah, has been built on the site of the church. Some of the ruins of the church are preserved beneath the mosque. In general, houses in the village are built on top of ancient ruins and caves. During the Crusader era, Casale Zacharie, like nearby al-Khidr, probably was a Christian village, and it was granted with al-Khidr to the church of Bethlehem between c. 1155 and c. 1186. Pottery fragments from the Mamluk era have also been found.
In the Ottoman census of 1538-1539, Bayt Dhakariyya was located in the nahiya of Halil, while in 1557, it was noted that the village revenues went to an Imperial imaret in Jerusalem. In 1852, Edward Robinson noted Beit Sakarieh “on an almost isolated promontory or Tell, jutting out northwest between two deep valleys; and connected with the high groundsouth by a low neck between the heads of those two valleys." An Ottoman list from about 1870 notes a Muslimwali, dedicated to a SheikhZakarja, located under a large tree. Several cisterns were also noted, and that the old Roman road to Jerusalem passed by. The PEF's Survey of Western Palestine visited in 1873 and noted: "From the main Roman road on the south a path leads to this ruin, situate on the brow, overlooking deep valleys on the east and north. Beside the path is a square foundation about 50 feet side, of roughly-dressed stones. The remains on the hill-brow are those of a large modern village, with more ancient foundations. One wall consists of stones 4 1/2 feet long, 2 feet high, roughly dressed. There is also a mosque, with a portico on the west, sunk below the surface. On the north side of this portico a pillar is placed with a capital of basket-work, like the eighth centuryByzantine capitals. The shaft is 2 feet diameter. The mosque door was shut ; perhaps it may represent the site of the church which once stood at this place. Drafted stones with a rough boss were also found, and another capital, apparently Byzantine. To the west of the site are rock-cut tombs, now blocked. A tree grows over the Mukam, or mosque."
1948
On January 14, 1948, Arab forces led by Abd al-Qadir al-Husayni attempted to capture the strategic hill of Beit Zakariah, and thus to split Gush Etzion into two in preparation for its total conquest. However, Jewish forces defeated them in the Battle of 3 Shevat. The defeat had strategic implications for all of Palestine - as a result, Husseini cancelled his plans to attack Jewish communities, and focused on attacks on the roads.
Since the Six-Day War in 1967, Khirbet Beit Zakariyyah has been under Israeli occupation. After the Oslo Accords in 1995, 100% of Khirbet Beit Zakariyyah land was classified as Area C, under full Israeli control. According to ARIJ, Israel has confiscated land from Khirbet Beit Zakariyyah in order to construct six Israeli settlements:
