During his exile, he was captured by pirates before finding refuge () in the state of Epirus that had been founded by Michael I Komnenos Doukas. He was restored to his see after Thessalonica was recovered by Theodore Komnenos Doukas in 1224. When Theodore requested to be crowned emperor, however, Mesopotamites refused, out of loyalty to the exiled Patriarchate in the Empire of Nicaea, and left his see in self-exile. Theodore was eventually crowned by the Archbishop of Ohrid, Demetrios Chomatenos, sometime in April–August 1227. Mesopotamites must have abandoned his see by then. The see appears to have remained vacant for some time thereafter, until sometime after 1230, when a Bulgarian bishop, possibly called Michael Pratanos, was installed as a result of the Bulgarian hegemony over the rump Empire of Thessalonica following Theodore's defeat and capture at the Battle of Klokotnitsa.