Archaeologist Tuncer Bağışkan has written that the site was turned into a place of religious significance as part of efforts to consolidate Islamic faith in Cyprus.

In 1767, Giovanni Mariti, a visitor to Nicosia, recorded there being a masjid with no minaret alongside a tomb.

According to an inscription at the entrance of the mosque, a minaret was added, along with a minbar and a mihrab, by Abdullah Pasha in 1820/21, during the reign of Mahmud II, who is known for public improvements in Cyprus.

The first bombing took place on the night of 24 March 1962 and was at the time blamed on Greek Cypriot EOKA.

[3] Left-wing Turkish Cypriot journalists Ahmet Muzaffer Gürkan and Ayhan Hikmet writing for the local newspaper Cumhuriyet wrote that the bombing was carried out by the Turkish Resistance Organisation on 23 April 1962 and later met with Polycarpos Georgadjis, Greek Cypriot Minister of the Interior.

[7] Samuel Hardy, a specialist on art theft, lists the destruction of Bayraktar Mosque among ethnically-based incidents of intentional damage to cultural heritage during the Cypriot conflict.

[8] In February 1975, when UNESCO officials visited the mosque, they reported it to have been "totally vandalised", with "the minaret pulled down, the windows blocked, the roof in a state of collapse".