After the dissolution of the Soviet Union, in the summer of 1993, Maskhadov took part in raids on the armed opposition against the government of Dzhokhar Dudayev in the Urus-Martan, Nadterechny, and Gudermes districts.

Maskhadov commanded the city from the Presidential Palace in Grozny, where on one occasion a Russian bunker buster bomb landed 20 meters from him but failed to explode.

In June 1996, at the negotiations in Nazran, Ingushetia, Maskhadov, on behalf of the ChRI administration, signed the Protocol of the Commission's Meeting on Ceasefire and Measures to Resolve the Armed Conflict in the CRI.

[3] By the end of 1996, when Maskhadov assumed his office, nearly half a million people (40% of Chechya prewar population) had been internally displaced and lived in refugee camps or overcrowded villages.

[7] Maskhadov survived assassination attempts on his life three times, on 23 July 1998 and 21 March and 10 April in 1999, in which the attackers used anti-tank missiles and bombs.

Maskhadov was one of the main commanders in the Battle of Grozny (1999–2000) along with Shamil Basayev, Ruslan Gelayev, Ibn Al-Khattab, Aslambek Ismailov, and Khunkarpasha Israpilov.

As Maskhadov and his men retreated, they set up a vast amount of booby traps and landmines to hinder Russian forces and make most of Grozny impassable.

Maskhadov offered his readiness for unconditional peace talks with Moscow several times in 2000 alone, continuing in the following years, but his appeals for a political solution were always ignored by the Russian side.

Maskhadov often denied responsibility for the increasingly brutal terrorist acts against Russian civilians by Basayev's followers, continually issuing denunciations of such incidents through spokesmen abroad, such as Akhmed Zakayev in London.

However, on 24 October 2002, radio communications were intercepted from Maskhadov's messages wherein he called for intensification of terrorist activities and sabotage in Russian territory.

[7] Evidence for Maskhadov's complicity in the 2002 Moscow theater hostage crisis was provided by its two principal perpetrators, Movsar Barayev and Abu Said.

[7] He described the rebels behind the Beslan school siege as "madmen" driven out of their senses by Russian acts of brutality and called the terrorist attack an atrocity.

Umar Khambiev, his designated negotiator, said that the separatists were no longer seeking independence, but only "guarantees for the existence of the Chechen nation".

[17] According to an official one announced on 8 March 2005 by the head of the Federal Security Service of the Russian Federation (FSB) Nikolai Patrushev, less than a month after Maskhadov announced the cease-fire,[18] a special forces unit of FSB had:[19]"… carried out an operation in the settlement of Tolstoy-Yurt, as a result of which the international jihadist and leader of armed groups Maskhadov was killed, and his closest comrades-in-arms detained.

[19] Akhmed Zakayev, one of his closest allies who acted as his spokesman and foreign minister, told a Russian radio station that it was probable that Maskhadov had indeed been killed; he indicated later that a new Chechen leader could be chosen within days.

According to ballistic evidence at their trial in the Supreme Court of the Chechen Republic, Maskhadov was allegedly killed by a shot from the pistol of Viskhan Hadzhimuradov, his nephew and bodyguard.

[22][20] A year later in 2006, a son of Maskhadov, Anzor, in an interview with Caucasian Knot allegedly claimed that his father was tracked down by a phone IMEI within 2 days before the raid took place.

[20] Shortly after a standoff with Russian special forces he fired his hand weapon and then hit by a stun grenade and then shot dead.

[23][24] In 2006, they lodged a complaint to the Parliamentary Assembly of the Council of Europe on "illegal" refusal by Russian authorities at the time to return Maskhadov's body back to the family.