The earliest recorded date in the construction of the bazaar is 1603, but the agglomeration of structures that exists today is the product of centuries of development. Several building phases are evident on stylistic and structural grounds.

Several long arterial streets covered with brick vaults make up the bazaar's structural core. These streets are lined with shops, often surmounted by a second story that opens onto the vaulted street via a balcony or screened window. Smaller streets link these larger arteries together. The intersection of two arterial streets or the entry point for large complexes along these streets is often marked with a larger vault or dome. These crossroads are known as chahar-su (meaning four suqs, or markets). In addition to shop stalls, the bazaar streets give onto mosques, madrasas, baths and warehouses. Two types of warehouses are present. The first is the caravanserai, usually composed of a large courtyard surrounded by cells and entered through an iwan portal. Smaller warehouses known as timchahs consist of a vaulted hall with rooms or shops around it. Together, these elements form an amorphous network of streets, shops and larger complexes that blend into the surrounding city.

The entrance to the bazaar is a monumental iwan-style gate opening onto the north side of the Maydan-i Imam known as the Qaysariyya Gate. This gives onto a wide vaulted market street that runs roughly south to north from the maydan in a straight line. Along this street, one passes through a domed chahar-su with entrances to the royal caravanserai (saray-i shah) on the west and the royal mint (zarrabkhana) on the east. Further north, this street is crossed by another arterial street running east-west under a more elaborate chahar-su. The grid formed by these streets and adjoining complexes is the most formally arranged part of the bazaar, and it is no coincidence that this also represents one of the oldest sections.

The bazaar's second main arterial path begins at the northeast corner of the maydan and winds its way northeast, finally reaching the southwestern end of the great mosque.