In 1546 he was appointed Metropolitan of Caesarea by his personal friend Patriarch Dionysius II of Constantinople, who sent him to Venice mainly to raise funds, but Metrophanes went also to Rome and met the Pope.
In 1548 this news caused a great concern in a part of the Greek population of Constantinople, with riots and an attempt to murder Dionysius II who was considered as guilty as Metrophanes.
As our Lord Jesus Christ in the Gospels said do not oppress or accuse anyone falsely; do not make any distinction or give room to the believers to injure those of another belief".
After his deposition, to grant him a financial revenue, he was appointed bishop eis zoarkeian (i.e. without pastoral obligations) of Larissa and Chios, and he returned to live in the Monastery of the Holy Trinity in the island of Chalki, near the capital.
Six years later, after the execution of Michael Kantakouzenos Şeytanoğlu and the murder of the Grand vizier Sokollu Mehmed Pasha, Jeremias II lost his supporters and Metrophanes III was successfully restored on the throne on 25 November 1579.