Under President Hissein Habre, members of Gourane, Zaghawa, Kanembou, Hadjerai, and Massa ethnic groups dominated the military. Idriss Deby, a member of the minority Zaghawa-related Bidyate clan and a top military commander, revolted and fled to the Sudan, taking with him many Zaghawa and Hadjerai soldiers in 1989. The forces that Deby led into N'Djamena on December 1, 1990 to oust President Habre were mainly Zaghawa (including a large number of Sudanese), many of whom were recruited while Deby was in the bush. Deby's coalition also included a small number of Hadjerais and southerners.

Chad's armed forces numbered about 36,000 at the end of the Habre regime but swelled to an estimated 50,000 in the early days of Idriss Deby. With French support, a reorganization of the armed forces was initiated early in 1991 with the goal of reducing the size of the armed forces. An essential element of this effort was to make the ethnic composition of the armed forces reflective of the country as a whole. While the military's size has been reduced to approximately 25,000 soldiers, leadership positions are still dominated by the Zaghawa.

War and rebellions have tapered off in recent years,. Following Idriss Deby's rise to power, Habre loyalists continued to fight government troops and rob civilians around Lake Chad. In the mid- and late-1990s, a rebellion in the south by the FARF delayed the promised oil development until crushed by government forces. Most recently, The Movement for Democracy and Justice in Tchad (MDJT) launched the most serious threat to Deby's hold on power, but little progress was ever made on either side. In January 2002, the government and the MDJT signed a formal peace accord. Although still slightly active, the rebellion has withered as of late 2003..