In the Medieval Age, the city was captured first by the Rashidun Caliphate in 637, by the Byzantine Empire in 969, by the Seljuk Turks in 1084, by the Crusades in 1098, and by the Baibars of the Mamluk Sultanate in 1268.

[4] Wendy Mayer and Pauline Allen suggest that the mosque is built on top of the former church of Cassian,[5] however this remains uncertain as Yaqut al-Rumi mentions a shrine of Habib as a place of pilgrimage at the beginning of the thirteenth century when Antioch was under Frankish rule which was not that same church.

[dubious – discuss] Muslims believe he was martyred for calling people to the religion of Allah.

He is referred to in the Quran, chapter Ya-Sin, verses 20–27, as the supporter of the disciples calling the people of Ya-Sin to the worship of the One God: "Then there came running, from the farthest part of the City, a man, saying, 'O my people!

'"[Quran 36:20-21] The two sarcophagi found in the yard of the mosque are believed to belong to Jonah and John the Baptist,[3] or the tomb of Habib along with that of Sham'un Al-Safa (Saint Peter, also known as Simon the Pure).