Returning from a fact-finding trip to the Greek Orthodox Archdiocese in America in 1930, Metropolitan Damaskinos recommended to Pat. Photios II that he appoint Metr. Athenagoras to the position of Archbishop of North and South America as the best person to bring harmony to the American diocese. The patriarch made the appointment on August 30, 1930.
When Archbishop Athenagoras assumed his new position on February 24, 1931, he was faced with the task of bringing unity and harmony to a diocese that was racked with dissension between Royalists and Venizelists who had virtually divided the country into independent dioceses. To correct this he centralized the ecclesiastical administration in the Archdiocese offices with all other bishops serving as auxiliaries, appointed to assist the archbishop, without dioceses and administrative rights of their own. He actively worked with his communities to establish harmony. He expanded the work of the clergy-laity congresses and founded the Holy Cross School of Theology. Through his capable leadership he withstood the early opposition and gained the love and devotion of his people.
On November 1, 1948, Archbishop Athenagoras was elected Patriarch of Constantinople. He was honored to be flown to Istanbul to assume his new position in the personal airplane of the American president Harry Truman. As patriarch, he was actively involved with the World Council of Churches and improving relations with the Bishop of Rome.
He died in Istanbul (Constantinople) on July 7, 1972.
His meeting with Pope Paul VI in 1964 in Jerusalem led to rescinding the 1054 excommunications of the East-West Schism. This was a significant step towards restoring communion between Rome and Constantinople. It produced the Catholic-Orthodox Joint declaration of 1965, which was read out on December 7, 1965, simultaneously at a public meeting of the Second Vatican Council in Rome and at a special ceremony in Istanbul. The declaration did not end the 1054 schism, but showed a desire for greater reconciliation between the two churches, represented by Pope Paul VI and Ecumenical Patriarch Athenagoras I. Nevertheless, not all Orthodox leaders at the time were happy with this Catholic-Orthodox Joint declaration, e.g., Metr. Philaret's 1965 epistle to the patriarch.
Equally unpopular to both Orthodox and the Papacy was his acceptance of the special relationship that exists between the Orthodox, specifically Greek, and the Melkite Greek Catholic Church, wherein the Melkites never severed their ties with the Orthodox, and consider their church an especially unique bridge between the separated Churches due to its Patriarchal nature, and the culture of the Near East where the East-West Schism is treated by the laity and many clergy as if it had never happened.