During the Balkan Wars of 1912–13 he served as company and battalion commander in the 6th Infantry Regiment, being wounded in the Battle of Sarantaporo. In August 1916 he joined Eleftherios Venizelos' Provisional Government of National Defence in Thessaloniki, and was charged with the formation of the 5th Regiment of the new Archipelago Division. Tsimikalis led the regiment to the front in May 1917, and fought with distinction in the Macedonian front, particularly in the Battle of Skra-di-Legen in May 1918, where the 5th Archipelago Regiment led the main assault on the Bulgarian positions.