The Great Mosque of al-Mutawakkil was founded by Caliph al-Mutawakkil, who reigned (in Samarra) from 847 until 861. The al-Mutawakkil mosque was the second of two mosques built on the site, with the Great Mosque being built between 849-852 A.D. Except for its magnificent minaret, much of the second mosque lies largely in ruin (though the walls of the mosque are partly intact). For its time it was the largest mosque in the Islamic classical period, and in the world.

On April 1, 2005, the top of the Malwiya minaret was damaged by a bomb. Insurgents reportedly attacked the tower because U.S. troops had been using it as a sniper position. The blast left pieces of brick from the top of the minaret along its spiral ramp.