In recognition of his contribution in the Hesychast controversy, Patriarch Isidore appointed him Metropolitan of Heraclea in Thrace in 1347. However becoming a protégé of co-Emperor John VI Kantakouzenos, Bishop Philotheus spent most of his time in Constantinople. During his absence, the city of Heraclea fell prey to the rivalry of the Genoese and the Venetians. In 1351 the Genoese led by Paganino Doria sacked his episcopal see of Heraclea. It was only due to the intervention of Bishop Philotheus that a large number of the inhabitants which were imprisoned by the Genoese, were set free. Thereafter he preserved a firm personal antagonism against the Genoese for the rest of his life.