He joined the Uganda Army (UA) in 1967, possibly recruited on Amin's orders. By then, Amin had risen to deputy commander of the Uganda Army. In 1970 Maliyamungu was promoted to the rank of corporal and served as pay clerk for the Uganda Army Air Force at Entebbe. At the time, he was aiding Amin in secretly enlisting troops from the West Nile region and southern Sudan. These forces were trained in the Mabira Forest, and were part of Amin's preparations for a coup against President Milton Obote. Maliyamungu eventually learned of Obote's intentions to arrest Amin, and warned his relative, whereupon they accelerated their coup plans. He played a crucial role in Amin's subsequent coup against Obote, and it was later claimed that he had rammed an armoured personnel carrier into an important armoury in the capital Kampala during the coup, ensuring that the putschists had access to necessary weapons. Another putschist, Moses Galla, has disputed this story, and stated that he had been the driver of the APC. Maliyamungu's main task during the coup was to secure Entebbe airport. This he successfully did by driving a tank from the Malire Barracks to Entebbe, and shooting at the airport entrance. He killed two priests by chance, and caused a panic among the airport's guards. The loyalist resistance of Entebbe thus collapsed, allowing Maliyamungu to take control almost unopposed. His takeover of Entebbe impressed Amin, and Maliyamungu consequently won the favor of Uganda's new president.