He initially worked as a secretary of Boris Sarafov until 1903, but after realizing the real purposes of IMRO towards the Greek population, he travelled to Athens where he received military training. He then returned to his homeland joining the Greek Struggle for Macedonia, setting up a small armed group of Greeks from Strumica which initially acted near the Giannitsa Lake against the Bulgarian komitadjis. He cooperated with many chieftains, including Gonos Yiotas and Theocharis Kougas from Gidas. He later acted near his hometown, in the wider Novo Selo area. Papaioannou had been successful in recruiting men from the area, however, one of the recruits had an Exarch father-in-law by the name of Peche, who immediately notified the Ottomans of their location. Papaioannou and his men were encircled but miraculously managed to escape with only one casualty.