He returned in his second year without finishing his studies, having been summoned back to command troops in Tindouf at the height of the Moroccan-Algerian conflict over the Western Sahara issue.
He rose rapidly through the ranks, and, by 1988, he was a ground forces commander at Ain Naadja in Algiers, where he played a significant role in suppressing the "Black October" riots.
In his memoirs, he recounts his hostility during this period to the interim prime minister Mouloud Hamrouche and president Chadli Bendjedid, whom he accuses of effectively "conniving" with the Islamic Salvation Front for the sake of increasing their power.
After the Islamic Salvation Front's electoral victory in 1991, he, along with Larbi Belkheir, was among the leading generals who decided to depose then-President Chadli Bendjedid and annul the elections, marking the beginning of the Algerian Civil War.
In October 2001, Khaled Nezzar's son Lotfi violently attacked a Le Matin reporter, Sid Ahmed Semiane, for having criticized his father.
Souaidia had accused him of "being responsible for the assassination of thousands of people", blaming him and other generals for starting the war and committing massacres attributed to the Armed Islamic Group.