The historic mosque has five domes in total, three of these are located in the main courtyard as free standing structures. The largest is located over the main prayer hall of the mosque.

circa 770 CE

Dome of the Ablution Fountain
The Dome of the Ablution Fountain (Qubbat al-Wudu) was first established during the Abbasid era. The current structure dates back to the Ottoman era, when it was reconstructed, on the orders of Osman Pasha Alkargi, after it was extensively damaged in the 1759 earthquake. Located in the middle of the courtyard, it has an octagonal base.

circa 780 CE

Dome of the Clock
The Dome of the Clock (Qubat ul-Awqat) was first built in the eastern section of the mosque by al-Fadl ibn Salih ibn Ali, who was the Abbasid governer of Damascus at the time. The dome is named after the funtion it was supposed to carry out, when the Ottomans transferred the mosque's clock here.

The dome rests on an octagonal base mounted on eight columns. The columns are topped with white marble capitals. The decoration of each column differs from the other, and the capitals are topped with pyramidal stones. The columns had bases of white marble of the old style, and ornate timber covered the wooden octagon from the inside, and consisted of coiled plant branches emerging from cups carved in the corners of the octagon. It is made of thick wooden bridges, and its roof at that time resembles a high cowl.

circa 790 CE

Dome of the Treasury
The Dome of the Treasury (Qubat ul-Khazna), was used to house the mosque's funds. Also built on the orders of al-Fadl ibn Salih ibn Ali Abbasid governer of the city towards the second half of the second century Hijrah. The dome used to hold the mosque's large endowments. Some Greek, Latin, Syriac, Coptic, Hebrew, Aramaic, and Georgian old manuscripts were also housed in Qubbat al-Khazna in the past.

circa 1894 CE

Dome of the Eagle
The Dome of the Eagle (Qubat ul-Nisr), located atop the center of the main prayer hall, is the largest of all the domes. Overlooking the old city of Damascus, with its gabled transept and rich front façade, it is among the most prominent and sublime features of the historic mosque. The original wooden dome was replaced by one built of stone following the 1893 CE fire. With a total height of 118 feet, it receives its name because it is thought to resemble an eagle, with the dome itself being the eagle's head while the eastern and western flanks of the prayer hall representing the wings. The dome rests on an octagonal substructure with two arched windows on each of its sides.

The Arab historian Ibn Jubayr wrote that whoever looks at this dome from a certain distance has the impression of seeing an eagle, whose head is formed by the cupola, its body by the prayer hall, and its wings by the walls on its right and left.

circa

Dome of Yahya's Shrine
It is a small dome atop the Maqam Nabi Yahya (Shrine of prophet Yahya). This shrine is located is located inside the main prayer hall of the mosque.