The earliest building on the site was a small shrine of the 11th dynasty (2081–1938 BCE), of which only the foundations remain. The shrine was later much enlarged by Hatshepsut and Thutmose III as a temple dedicated to the local form of Amon and the primeval Ogdoad (group of eight deities of the creation myth in Middle Kingdom (Egypt, ancient) Egypt 【1938–c. 1630 BCE】). When Ramses III erected his mortuary temple in the vicinity, the enclosure walls incorporated the smaller temple inside the precinct. Madīnat Habu, as a fortified site, offered security during the late New Kingdom (Egypt, ancient) (1539–1075 BCE) to the inhabitants of western Thebes during times of unrest and served as the administrative centre for the women's village at Dayr al-Madīnah.

Ramses III's temple fell out of use during the Third Intermediate Period (Egypt, ancient) (1075–656 BCE), when it became a cemetery for private burials. A row of funerary chapels was erected just inside by the God's Wives of Amon during the 25th and 26th dynasties (see ancient Egypt: The 24th and 25th dynasties (Egypt, ancient) and ancient Egypt: The Late period (Egypt, ancient)). The small temple of Amon was enlarged by the Kushite rulers and then much expanded during the Ptolemaic dynasty (Egypt, ancient), with the addition of a colossal pylon and a renovation of the processional axis. The final addition was an open court dedicated by the Roman emperor Antoninus Pius. During the 1st millennium CE, a thriving Coptic town, Djeme, grew up within the fortified walls of Madīnat Habu.