Because of his activism, in 1896 the Ottoman authorities dethroned him as Armenian Patriarch of Constantinople and exiled him to Jerusalem. He returned briefly from exile in 1908 after the Committee of Union and Progress declared the restoration of the constitution in 1908 and was reelected as Patriarch of Constantinople for a few months. After the death of Catholicos Khrimian, Izmirlian was elected as Catholicos of All Armenians as Matthew II and left for Etchmiadzin for his consecration. He held the post of Catholicos of All Armenians for three years before he died. During his tenure, he became the first Catholicos to make a pilgrimage to Ani, the ruined capital of medieval Armenia.