It was completely destroyed with pre-planted explovises at the beginning of the Bosnian War in 1992 by the VRS, and levelled to the ground; along with the left over stones and rubble from the mosque being hidden all over Foča to prevent its reconstruction.

The mosque was erected in 1549 by Hasan Nezir, the Ottoman Persian supervisor of state goods and finance in Bosnia and a close associate of Mimar Sinan.

The ornamentation is in typical Ottoman classical architectural style, and since it was the first mosque of its kind in Bosnia and Herzegovina, its design was emulated by many others that were later built.

In October 2018, the Bosnian State Court charged Goran Mojović for crimes against humanity, including the destruction of the Aladža mosque.

According to the prosecutor, in the course of a widespread and systematic attack by the Bosnian Serb military, paramilitary and police forces against the civilian population of the city of Foča, on the evening of 2 August 2 1992, Mojović, as head of the local engineering unit of the Army of Republika Srpska, gave the order to destroy the mosque, and - despite the refusal of two other soldiers - together with Rajko Milošević detonated the mosque with about 25 anti-tank mines.

[1] The reconstruction of the mosque in line with the original plans was carried out between 2014 and 2018 under supervision of the Commission to preserve national monuments of Bosnia and Herzegovina.