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, when besides the mosque was repaired even the courtyard building next to it. The Minister of Education and Church Affairs sent to the State Council of the Principality of Serbia a document dated May 10, 1868, with the following content: “In order for Mohammedans, who are on their business in Belgrade, not to be without religious consolation, His Excellency ordered the one of the local mosques to be repaired for their place of worship. Due to this high order, “Bajrak” mosque was chosen as the most appropriate one and the Minister of Construction as at my request sent the professional people to examine the same mosque, and a house next to it, where the mullahs will reside….”

By the Decree of Prince Mihailo Obrenović from May 1868, The Minister of Education and Church Affairs was authorized to “give to khoja 240, and a muezzin 120 talirs a year”, and the servants of the mosque had even income from real estate – waqf property. The first imam and the muezzin at the Bajrakli Mosque were appointed in 1868.

Between the two world wars, the mosque was restored even by the Municipality of Belgrade, when in 1935 it was protected for the first time by the Regulation on the Protection of Antiquities in Belgrade. The restoration was performed several times and after the Second World War by the National Committee of the City of Belgrade and by the Cultural Heritage Preservation and Scientific Research Institute and, from the mid sixties of the 20th century even by the Cultural Heritage Preservation Institute of Belgrade. After the recent damage in 2004 conservation works on rehabilitation and restoration of stone facades with the restoration of window openings were carried out.