All club football in Greece was suspended from 1941 to 1945 due to the German occupation of the country. After the war period, the club was constantly competing with Aris for the Thessaloniki championship, which gave upon its winner the right to participate in the Greek championship. Iraklis participated in the 1947 Greek Cup final, where was defeated 5–0 by the dominant Greek team of that era, Olympiacos. In the 1950s, the team solidified its position among the top teams in Greece along with Olympiacos, AEK Athens, Panathinaikos, Aris and PAOK. Nevertheless, the club struggled with financial difficulties in an ailing Greek economy. Thessaloniki (where many refugees from the Greco-Turkish War of 1919–1922 had settled) was particularly damaged by the economic downturn. The highlight of the decade was the 1957 Greek Cup final, in which Iraklis was once again defeated by Olympiacos, 2–0.