John was the eldest son of Theodore Komnenos Doukas and Maria Petraliphaina. In 1230 his father was captured together with his family in the Battle of Klokotnitsa by Ivan Asen II of Bulgaria. When his sister Irene married Ivan Asen II in 1237, John was released from captivity together with his now blind father Theodore and his younger brother Demetrios. Theodore and his sons made their way back to Thessalonica and incited a revolt against Theodore's brother Manuel Komnenos Doukas who had ruled the city since 1230. Since Theodore was blind, he installed his son John as ruler and retired to Vodena.