After the war, Lembong returned to Indonesia as KNIL officer in January 1946 and later joined an irregular armed organization called the "Loyalty of the Indonesian People from Sulawesi" () after Operation Product in 21 July 1947. This group was mostly made up of men from the Minahasa region in North Sulawesi who were residing in Java. In 1947, KRIS and other groups were integrated into the Armed Forces of the Republic of Indonesia (). In 1948, TRI became the National Armed Forces of Indonesia () and Lembong became commandant of 16th Brigade (Brigade XVI) with the rank of lieutenant colonel. During Operation Kraai, Lembong was captured in Yogyakarta and jailed by the Dutch for a time in Ambawara.