Polymenakos continued as regimental commander during the Second Balkan War against Bulgaria, seeing action at Nevrokop, Prendel Han and Mehomia.

[2] In 1921 he commanded the III Army Corps in Anatolia, and he led it in the Greek summer offensive and the advance towards the Sakarya River.

[2] In May 1922, he was considered for the post of commander-in-chief of the Army of Asia Minor after the retirement of Lt. General Anastasios Papoulas, but the monarchist government mistrusted his political credentials and passed him over in favour of Georgios Hatzianestis.

In June, despite the imminent Turkish offensive, he asked to be removed from his position due to his disagreements with the government on the pursuit of the war.

Thus Polymenakos was appointed commander-in-chief on 24 August 1922, having barely enough time to lead the evacuation of the last remnants of the Greek forces from Anatolia.