Following a independence referendum that took place from 29 February to 1 March 1992, the People's Assembly of Bosnia and Herzegovina declared independence from Yugoslavia. Mahmuljin was subsequently appointed to the General Staff of the newly created Army of the Republic of Bosnia and Herzegovina (; ARBiH). Two of Mahmuljin's brothers, Omer and Nagib, were killed at the Omarska camp, near Prijedor, which was operated by the Army of Republika Srpska (; VRS) from May to August 1992. In December 1993, Mahmuljin commanded ARBiH units attempting to seize the Vitezit ammunition factory in Vitez from the Croatian Defence Council (; HVO). "By taking that factory, we would be self-sufficient in weapons production," Mahmuljin told the reporter Chuck Sudetic, adding that the ARBiH had already reached the factory's perimeter. He dismissed threats by local HVO officials to blow up the factory rather than let it fall into the hands of the ARBiH, arguing that such a move would result in an "environmental calamity" that would spell "the end for the 15,000 people in Vitez." In September 1994, Mahmuljin was appointed as the commander of the ARBiH 3rd Corps, replacing previous commander Kadir Jusić.
