In 2001, after the outbreak of the Second Chechen War, Khangoshvili joined the armed resistance of the Chechen Republic of Ichkeria in their fight against Russia. Khangoshvili was a field commander and had close ties to former Chechen president Aslan Maskhadov. Maskhadov was killed in March 2005 in a raid by the FSB, Russia's domestic intelligence agency. According to Khangoshvili's brother, Zurab, Zelimkhan participated in the June 2004 attack on security, military and police forces in the Russian Republics of Ingushetia and Dagestan, in which 88 police officials and civilians were killed; Zelimkhan was reportedly wounded in the leg during the operation. Russian President Vladimir Putin claimed that he was one of the perpetrators of a Moscow metro bombing. However, Zelimkhan himself denied that he was ever responsible for war crimes, telling Georgian media, "The Russians are blaming me for many things, including terrorist attacks. This is a lie. No one can provide any evidence that a single civilian was injured or killed in any of my actions!".