[2][3] During the First Nagorno-Karabakh War, Aghdam was used by Azerbaijani forces to fire BM-21 Grad long-range missiles at the Armenian populace of Stepanakert.

[7][8][9][10] A narrative of "barbarous Armenians who turn mosques into pigsties" would become an important component of mobilization in Azerbaijan in the prelude to the 2020 Nagorno-Karabakh war.

[14] A satellite investigation conducted by the Caucasus Heritage Watch of Cornell University found that between 1977 and 2019, the structure and shape of the mosque remained unchanged.

Since 1992, the mosque sustained minor damage under Armenian control, with only the modern roofing installed during Soviet times being removed.

[16] Three days later, president Ilham Aliyev and first lady Mehriban Aliyeva visited the ruins of the city and the Aghdam Mosque.