In 1223, he was selected by the Nicaean emperor John III Vatatzes to fill the seat of the Ecumenical Patriarchate, which had relocated there after the fall of Constantinople. Germanus assumed the patriarchal throne on 4 January 1223, and quickly proved himself a valuable ally to Vatatzes. Throughout his patriarchate, Germanus strove to re-establish his authority as the head of the politically splintered Orthodox world, all the while supporting Vatatzes' in his claim to the Byzantine imperial inheritance. Thus Germanus clashed with the prelates of Epirus for their support of the Epirote rulers, and especially the Archbishop of Ohrid, Demetrios Chomatenos, who had presided over the coronation of Theodore Komnenos Doukas as emperor at Thessalonica, directly challenging Nicaea's position. After the Epirote defeat at Klokotnitsa in 1230 however, the Epirote bishops were gradually won over; in 1232, the schism was healed with the Epirote church recognizing his authority, followed by a tour of the region by Germanus in 1238.