Pope Vigilius was in Constantinople when Eutychius became patriarch. Eutychius sent him the usual announcement of his own appointment and a completely orthodox profession of the then-united
Catholic faith. At the same time, the Pope urged him to summon and preside over the Church Council summoned to deal with the
Three Chapters Controversy. Vigilius first gave, and then withdrew, his consent to the Council. In spite of the Pope's refusal, the council met on
5 May 553 at Constantinople, and Eutychius shared the first place in the assembly with the
Apollinarius of Alexandria and Domninus, called
Domnus III of Antioch. At the second session, the pope excused himself again on the grounds of ill health. The subscription of Eutychius to the Acts of this synod, which was later recognized as the
Fifth General Council and which concluded on
2 June 553, is a summary of the decrees against the Three Chapters.
Eutychius had, so far, stood by the Emperor throughout. He composed the decree of the Council against The Chapters. In
562, he consecrated the new church of
Sancta Sophia. However, Eutychius came into violent collision with Justinian in
564, when the Emperor adopted the tenets of the
Aphthartodocetae, a sect of Egpytian
Monophysites who believed that
Christ's body on earth was incorruptible (’aphthorá) and subject to no pain.
Eutychius, in a long address, argued the incompatibility of the Aphthartodocetic beliefs with Scripture. Emperor Justinian insisted that he subscribe to it anyway. When Eutychius refused to compromise, Justinian ordered his arrest. On
22 January 565, Eutychius was celebrating the feast day of
St. Timotheus in the church adjoining the
Hormisdas palace when soldiers broke into the patriarchal residence, entered the church, and carried him away.