The architecture of the mosque belongs to the type of one-storey cubic building with a dome and minaret. With massive walls and small openings. It was built of stone, and some segments were carried out in brick and stone.

The building has the square plan, while the octagonal dome is supported by oriental domed arches and niches -trompes, with modest decoration of consoles.
The number of windows on the facades is uneven, while the one is located on each side of the tambour of the dome.

Dome supporting elements and all the openings on the building end in characteristic ogee oriental arches. 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. Opposite to the entrance, in the interior of the mosque, there is
the most sacred space – the mihrab, a shallow niche with elaborate vault decoration, set in the direction of the holy city of Mecca to the southeast, while the raised wooden pulpit (minbar) is set to the right of the mihrab, in the south-west corner.

Above the entrance, there is a wooden gallery (mahfil) from which one can come to the serefa, terrace on the minaret. Interior decoration of the mosque is very modest. The walls are without plaster with shallow moldings, rare stylized
floral and geometrical motifs and calligraphic inscriptions of verses from the Muslim holy book Koran, then with the names of the first righteous religious leaders caliphs, as well as of the God’s i.e. Allah’s magnificent properties and names written in Arabic letters on a specially decorated carved panels levhas.

At the entrance to the mosque there was an arched arcade porch with three small domes. There is a fountain for prayer washing in the yard, as well as an  uncompleted religious school (madrassa) with the library. The Bajrakli Mosque is the main Islamic cultural centre in Belgrade. Today the mosque is a bit hidden in the environment of higher housing units in Gospodar Jevremova Street.

Because of its antiquity, rarity, preservation of the original purpose and representativeness of religious architecture and Islamic culture, in 1946 was placed under state protection as a cultural monument, and in 1979 was declared cultural monument of great value.