Eugenius was among the Archbishops held as hostages by Mahmud II along with Patriarch Gregory V when the Greek War of Independence broke out in 1821. On 10 April 1821 Gregory V was deposed and hanged by the Turks in the central gate of the Ecumenical Patriarchate. Archbishop Eugenius, still a prisoner at the time, was elected as the new Patriarch under the name Eugenius II.