In 1942, he was elected into the Central Committee of the Communist Party of Greece and was named supervisor of the Macedonia wing of the Greek People's Liberation Army (ELAS).

[4] In November 1944, his forces liberated Central Macedonia and helped save thousands of Greek Jews from imminent peril from the exiting Nazi regime.

In February 1946, Markos Vafeiadis disagreed with Nikos Zachariadis, the general secretary of KKE, who wanted to create a standing communist army.

After the end of Joseph Stalin's era, Markos Vafeiadis was restored into KKE and was elected as a member of the Political Bureau of the Central Committee of the party.

Ηe became a political supporter of Andreas Papandreou and in November 1989 and April 1990, he was honorarily elected into the Greek parliament through the nationwide list of the Panhellenic Socialist Movement (PASOK).