The mosque is the result of continual construction, reconstruction, additions and renovations on the site from c. 771 CE to the end of the 20th century.

[2] The Seljuks modified the relatively uniform and egalitarian form of the hypostyle building, first by replacing the columns in front of the mihrab (on the south side of the mosque) with a large domed space in 1086–87.

[8][7] It also introduced a new type of squinch, consisting of a barrel vault placed above two quarter-domes, which was copied in other mosques shortly afterward.

[8] This was an early appearance of the muqarnas technique (a three-dimensional geometrical composition of niches), which had been developing around this period.

[4]: 53–54  The domed space may have been intended to act as a maqsura, an area reserved for the sultan and his entourage during prayers.

[4]: 56  These transformations resulted in giving the mosque its current four-iwan form, a type of layout which subsequently became prevalent in Iran and other parts of the Islamic world.

[7][8] Some of this work was probably done in the late 11th or early 12th centuries, but the chronology of construction here is unclear and many vaults likely date from different periods of repair and renovation.

[7][2][9] It's uncertain if the earlier minarets of the mosque were preserved until this time, but no historical texts make reference to them after the mid-11th century.

[2][7] Under the Ilkhanid sultan Uljaytu (r. 1304–1317), the arcade around the sides of the courtyard was vertically divided into two levels, as it appears today.

This hall is covered by a series of remarkable transverse vaults, while its southern wall features an elaborately-carved stucco mihrab dated to 1310.

In particular, the rich tilework covering the façade of the southern iwan today was originally added under the patronage of the Aq Qoyunlu ruler Uzun Hasan in 1475–6.

[2] Most Safavid rulers did work on the mosque, except for Shah Abbas I who was more preoccupied with his new constructions around the Naqsh-e Jahan Square.

[4]: 53  During the Safavid era some parts of the prayer halls were also enlarged and new tile revetment were added to the iwans and minarets.

[2] The mosque today is an amalgamation of different styles and periods coalesced into one building, the details of which cannot always be easily dated.