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Effects of war and financial struggles (1991–2008)

On 23 July 1993, during the First Nagorno-Karabakh War, the city of Agdam was seized by Armenian armed forces,^[11] and the team was forced to move from Imarat Stadium to Baku, while the head coach of the team, Allahverdi Bagirov, died in the war. Financial problems plagued the club during the period from 1998 to 2001, and the club went through hard times although it became the first Azerbaijani team to win away from home in a European competition by defeating the Israeli side Maccabi Haifa in the 1999 UEFA Intertoto Cup thanks to a double strike from club legend Mushfig Huseynov. Qarabağ has also represented Azerbaijan in the UEFA Cup Winners' Cup and UEFA Cup many times.

These problems were alleviated in 2001, when one of the largest holding companies of Azerbaijan, Azersun Holding, starting sponsoring the team. The squad used the name of Qarabag-Azersun for two seasons, but then returned its original name in 2004.