After the Asia Minor Disaster of 1922, Vafiadis went to Thessaloniki and Kavala as a refugee. From 1928, he worked in Thessaloniki as a member of the "Federation of Greek Communist Youths" (OKNE). In 1932, he was jailed and exiled for his political work. After his release in October 1933 he worked as party instructor in many areas of Greece.
At the beginning of the Metaxas's dictatorship (August 4, 1936) he was exiled in the island of Agios Efstratios, but escaped in less than a month. Subsequently he worked in the party's underground organisation in Crete and was one of the leaders of the Chania uprising against the dictatorial regime (July 28, 1938). After the supression of the uprising, he went to Athens where he was arrested. He was jailed in Akronafplia and exiled to the island of Gavdos.
The Civil War
In May 1941, during the German invasion in Greece, he escaped from Gavdos and began underground work against the German occupation, initially in Crete, later in Athens and Thessaloniki. In 1942, he was elected into the Central Committee of the KKE and was named supervisor of the Macedonia wing of the "Greek Popular Liberation Army" (ELAS). In May 1944, he was elected as a representative of Thessaloniki to the national congress that took place at the village of Koryschades, which he was unable to attend.
In November 1944, he went into disagreement with Aris Velouchiotis, who wanted ELAS to prepare to fight the British and, when fighting did break out in December, the Macedonia wing of the ELAS did not fight the British troops. He also went into disagreement, in February 1946, with Nikolaos Zachariadis, the secretary general of the KKE, who wanted to resume fighting.
However, in July 1946, Zachariadis appointed him as leader of the communist guerrilla formations. In October 1946, when the General Command of the "Democratic Army of Greece" (DSE) was founded, he assumed its leadership, and in December 1947 he was appointed Prime Minister and War Minister of the "Provisional Democratic Government".
During the late stages of the Civil War his disagreement with Zachariadis on issues of military doctrine led to his removal from leadership (August 1948) and later from all offices (January 1949). In October 1950, he was ousted from the KKE, while he was in isolation in the Soviet Union, where he had fled after the breakup of the DSE.
After the end of Stalin's era, Markos Vafiadis was restored into the KKE and was elected as member of the Political Bureau of the Central Committee of the party. However, new disagreements with the party leadership led to his removal from office in January 1958 and to his second ousting from the KKE in June 1964. After the party split in 1968, KKE Interior restored him.