[16][15] Recent archeological studies have suggested that the present mosque stands over a part of what was previously the Roman forum of the city.

[17] According to traditional narratives, it also stands on the site of an earlier church built by the Byzantine emperor Heraclius in the 620s and dedicated to Saint Thomas.

[20][21][22] Stories of Christian churches being partitioned in this manner are a recurring motif in Muslim narratives about the early Islamic conquests.

[23][24] In the case of Diyarbakir, this story has been accepted by some scholars (e.g. Creswell) and is widely repeated by locals and in popular narratives of the mosque's history.

[27][24][22] Fatma Meral Halifeoğlu, Martine Assénat, and Jean-Charles Ducène have discounted the story as apocryphal.

[22] Among the other complications is the Zuqnin Chronicle, which records that the city's main church, built by Heraclius in 629, was fully restored by the Christian community in 770, long after the Muslim conquest.

[31] Nasir Khusraw wrote in 1045 that the city's main church was an impressive building that stood next to the mosque.

[47] The western and eastern wings of the mosque, which flank the main courtyard, are products of Inalid and Nisanid patronage in the 12th century.

[48] The eastern wing of the mosque, which also contains the main external entrance leading to the courtyard, bears an inscription dating it to 1163-1164, during the Nisanid period.

[47] The elaborately-decorated western and eastern courtyard façades are both notable for the use of spolia from older Byzantine buildings, including columns, Corinthian capitals, friezes with vine motifs, and pieces of Greek inscriptions.

They were created under the supervision of Hibatallah of Gurgan, the only recorded architect of the mosque, who also completed the prayer hall in 1155-1156.

[47][15][53][b] The courtyard façade of this madrasa is preceded by a portico incorporating spolia of thick antique columns.

[47] Later renovations include additions from the 18th century under the Ottomans, such as the stone used in the mihrab set in the middle of the qibla wall.

[40] Kufic inscriptions found on the building's exteriors record in detail the rebuilding and additions made to the complex throughout its long history.

The columns were originally thought to be structural, but later considered to be in place for either partial support or simply for decoration.

The aisles are divided in the middle by a large central nave which runs perpendicular to the qibla wall.

The courtyard façade is decorated with garland and meander motifs, as well as an inscription with floral Kufic calligraphy.

[60] Over the course of history, Turkey has altered the method of covering mosques with large domes, a tradition since the Ottoman period.

The Great Mosque of Diyarbakır also has thick pillars instead of the round columns[60] often found in Syria, and lacks certain ornamentation in its mosaics.