After his Indian campaign[1] in 1399, Timur (Tamerlane) decided to undertake the construction of a gigantic mosque in his new capital, Samarkand. When Timur returned from his military campaign in 1404 the mosque was almost completed. However, Timur was not happy with the progress of construction, and immediately had various changes made, especially on the main cupola.[2]

From the beginning of the construction, problems of structural integrity of the structure revealed themselves. Various reconstructions and reinforcements were undertaken in order to save the mosque. However, after just a few years, the first bricks had begun to fall out of the huge dome over the mihrab.[3] The scale of Timur's plans pushed the building techniques of the time to their limit, and the building's integrity was not helped by the rushed nature of its construction.[4][5]

In the late 16th century, the Abdullah Khan II (Abdollah Khan Ozbeg) (1533/4-1598), the last Shaybanid Dynasty Khan of Bukhara, cancelled all restoration works in Bibi-Khanym Mosque.[6] After that, the mosque slowly deteriorated and became a ruins gnawed at by the wind, weather, and earthquakes. The inner arch of the portal construction finally collapsed in an earthquake in 1897.[7][8] During the centuries the ruins were plundered by the inhabitants of Samarkand in search of building material, especially the brick of the masonry galleries along with the marble columns.

A first basic investigation into securing the ruins was made in Soviet times. Late in the 20th century, the Uzbek government began restoration of three dome buildings and the main portal. In 1974 the government of the then-Uzbek SSR began the complex reconstruction of the mosque.[9] The decoration of domes and facades was extensively restored and supplemented. During these restorations, a band of inscriptions revealing Surat al-Baqarah of the Quran was added to the main sanctuary iwan of the mosque.[10] As of 2016, work on the mosque restoration was ongoing.[11][better source needed]