Back in Congo-Brazzaville, Mondjo served as an army officer, and he was Director of Lessons and Studies at the Marien Ngouabi Military Academy in Brazzaville from 1987 to 1993. He sided with rebel leader Denis Sassou Nguesso during the June–October 1997 civil war; the war ended with Sassou Nguesso regaining power and ousting President Pascal Lissouba. In December 1997, Mondjo was appointed as Commander of Military Zone 1, which included the country's economic capital, Pointe-Noire; he remained in that post for five years. He was appointed as Chief of Staff of the Congolese Armed Forces on 20 December 2002, and he was promoted to the rank of major-general ("général de division").