John died at Limnia in 1297. John Lazaropoulos, in his "Logos", notes that when his son Alexios succeeded him, the western part of his realm was under heavy pressure from "the godless Agarenes" and only Kerasous, part of Chalybia, Oinaion, and "the thirteen towns or forts of Limnia" remained to the Empire; John may have been leading his forces against the enemy when he died. His body was transported to his capital and interred in the Panagia Chrysokephalos Church ("Golden-headed" Virgin). Portraits of John and his wife Eudokia could be seen in the church of St. Gregory of Nyssa, prior to its reconstruction in 1863. These portraits were notable that his robes were adorned with the single-headed eagle "the special emblem of the Comneni of Trebizond", while her robes bore the double-headed eagle of Byzantium.