Moutoussis, originally an Engineers officer, became one of the first six Greek officers in 1912 that were selected to receive aviation training in France, in order to man the newly established aviation branch of the Hellenic Army. In the following Balkan Wars (1912–1913) he initially carried out bombing missions on Turkish positions. At the beginning of December 1912, he was positioned in the Epirus front, where he performed various scouting and bombing operations in the region around Ioannina. At the end of the month he was ordered to move to the Aegean front of the war, where he took part in the Battle of Lemnos.