When he first arrived in FLN territory, he was subject to a thorough investigation to prove he wasn't a traitor.[2] News of Messaoudene's strong background as a NATO fighter pilot and Algerian loyalty reached then-Minister of War Krim Belkacem, who personally admitted Messaoudene into the FLN because he knew his family.[1] In the FLN, Messaoudene was entrusted to train young pilots in allied countries supporting the FLN such as the USSR, Yugoslavia, Egypt, China, and Iraq.[2] Messaoudene would use his piloting experience to drop supply parachutes and transport cargo from Algeria elsewhere.[1][2]
This strategy was developed due to Chinese and Soviet distaste in the idea of building an airbase in Libya to supply the FLN. Messaoudene led these raids and supply drops, and became the first activities of the Algerian Air Force.[3][4]
After Algerian independence, Messaoudene was appointed the first commander-in-chief of the newly-established Algerian Air Force.[5] During the Sand War in 1963, Moroccan aircraft struck Algerian troops moving from Béchar to Tindouf and then Tindouf to the border. The airbase in Bechar and one near Tindouf were controlled by France, who ordered Algeria not to use them. Messaoudene responded by ordering his planes further south.[1]
He was appointed advisor to president Houari Boumédiène until 1969, when he took over as the head of Air Algérie, succeeding the first company president Laroussi Khalifa.[6] Under Messaoudene, Air Algerie completed nationalization. Messaoudene held several ministerial positions in the 1970s and 1980s. From 1972 to 1977, he served as Minister of Posts and Telecommunications, from 1977 to 1978 as Minister of Health, from 1979 to 1984 as Minister of Light Industry, and as vice-president of the Algerian Parliament from 1987 and 1992.[1] In 1992, he retired from politics.[1]
Messaoudene died on January 1, 2009 after a long illness at the Ain Naadja Military Hospital in Algiers.[2] He was buried at El Alia Cemetery. His son Mohamed Seddik Ait Messaoudene was appointed Minister of Health on September 14, 2025.[7] Air Algerie renamed their headquarters in Bab Ezzouar after Messaoudene in 2024.[8]