During the occupation of Serbia by the Austrians (between 1717 and 1739), it was converted into a Roman Catholic church; but after the Ottomans retook Belgrade, it was returned to its original function.

It once dominated in the atmosphere of mostly ground floor houses in the busy commercial and craft town district of Belgrade, the so-called Zerek.

Descriptions of Belgrade of the 17th century were preserved by Ottoman travel writer Evliya Çelebi in which he vividly described the appearance of the town in the period of Turkish rule, with various buildings of Islamic architecture.

In the second half of the 19th century, the Bajrakli Mosque was described by historians and travel writers Konstantin Jireček, Giuseppe Barbanti Brodano, as well as by archaeologist and ethnologist Felix Kanitz.

It is assumed that today's Bajrakli Mosque was built on the place of an older mesdzid, probably in the second half of the 17th century, as the endowment of the Ottoman ruler Sultan Suleiman II (1687—1691).

In it, as in the main mosque, there was the muwaqqit, the man who calculated the exact time of AH according to the Islamic calendar (which began in 622, i.e. in the year of Hijrah, the year during which the flight of the Prophet Muhammad from Mecca to Medina) occurred to determine sacred days, regulated clock mechanism and put the flag on the minaret, to signal the simultaneous beginning of the prayer to other Islamic places of worship in the town of Belgrade.

In 1868, the Minister of Education and Church Affairs was ordered by Prince Mihailo Obrenovic to choose one of the existing mosques and enable it for the performance of Muslim religious rites.

The minaret - a thin tower with conical roof, with a circular terrace at the top, from which the faithful are called to prayer by the muezzin - is located on the northwest exterior side.