[2] According to historian Audrey Altstadt, Elchibey faced several major problems during his tenure as president: "the war in Nagorno-Karabagh (with loss of land and creation of refugees), inflation and related economic problems (including slow progress on an oil deal with foreign investors), and the remnants of Russian-Soviet control and influence of the old order.

After the Khojaly Massacre (26–27 February 1992), the fall of Shusha (8 May 1992) and Lachin (15–17 May 1992), the temporary Azerbaijani communist establishment led by Yaqub Mammadov could no longer hold power.

At the same time, Elchibey's government established the national Azerbaijani Navy and managed to reach an agreement with Russia on receiving one-quarter of the Soviet Caspian Flotilla based in Baku.

Upon his election, Elchibey appointed Isgandar Hamidov, a police colonel and the leader of the newly established Grey Wolves movement in Azerbaijan, as the Minister of Interior.

Hamidov, despite his personal devotion and contributions in capturing Agdere district of Azerbaijan, proved to be generally incompetent and resigned in April 1993 after the fall of Kalbajar.

[10] In June 1992, the Azerbaijani army started a counter-offensive codenamed Operation Goranboy in Nagorno-Karabakh, establishing control of over 40% of the region by the fall of 1992 and approaching within 7 kilometers of Shusha.

However, as the Azerbaijani offensive pushed further into Karabakh, it became further bogged down in controversy, mismanagement, corruption and treachery by Elchibey-appointed Defense Minister Rahim Gaziyev, along with the guerilla tactics of the NKR Army in mountain warfare.

[15] He also held some pan-Turanian views, for which he enjoyed the support of the leader of the Turkish Nationalist Movement Party, Colonel Alparslan Türkeş.

[19] On 12 September 1992, he paid a visit to Moscow, during which he signed, along with Boris Yeltsin, the Treaty on Friendship, Cooperation and Mutual Security between the Republic of Azerbaijan and the Russian Federation.

Aliyev quickly took control of the power, becoming the Chairman of the Azerbaijani parliament on 15 June 1993 and offering the prime ministership of the country to Huseynov.

He signed the Bishkek Protocol to cease hostilities on the frontline, and further solidified his power by organizing impeachment hearings and holding a national referendum on 29 August 1993, which formally stripped Elchibey of the presidency.