[6] During the Mamluk period from the 13th to 15th centuries, the lands and surplus agricultural produce of al-Muharraqa were dedicated as a waqf for the maintenance of the Dome of the Rock in Jerusalem and the Great Mosque of Gaza.

The villagers paid a fixed tax rate of 25% on a number of crops, including wheat, barley, beehives, and goats; a total of 26,600 akçe.

[9] In 1883 the PEF's Survey of Western Palestine found of archaeological remains at the place, called Khürbet Muntaret el Baghl, "a few scattered stones and ruined rubble cisterns on a slope.

[5] During the 1948 Arab-Israeli War, the village with Kawfakha was raided by the Palmach's Negev Brigade on May 27–28, and a correspondent for The New York Times reported it was officially captured on May 29.

[5] T'kuma, established in 1949, although the latter was built on lands belonging to the city of Gaza, but just 2 kilometers (1.2 mi) west of al-Muharraqa's village site.

Palestinian historian Walid Khalidi described the village remains in 1992:The site is overgrown with thorny plants and short grasses and surrounded by eucalyptus trees.

The cemetery, overgrown with wild vegetation, still exists, in a dilapidated condition, and the fallen superstructure of one of the tombs is visible.