John was the son of Theodore Komnenos Doukas, who was emperor in Thessaloniki until he was captured and blinded after the battle of Klokonitsa in 1230. John was also imprisoned at that time, but they were released in 1237 and set about retaking Theodore's throne. Since Theodore had been blinded, however, John took the throne instead, expelling his uncle, Theodore's brother, Manouel. Manouel was able to retake Thessaly in turn with Nicaean support. John was later forced to relinquish his claim to be emperor and accept the suzerainty of John III of Nicaea in 1242. John died two years later in 1244.

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