Emmanuel Metaxakis was born in Crete, in the commune of Christos, now part of the Ierapetra municipality.

In 1891, he became the hegumen of the Monastery of Bethlehem, and the Archbishop of Mount Tabor, Spyridon, ordained him a deacon with the name of Meletius.

The ruling which at last decided the issue was based on a document which had been drafted by Metaxakis and which had been published in the Gazette of the Cypriot government.

He organized the Statutory Charter of the Church of Cyprus and founded the periodical Ekklesiastikos Kirix ("Ecclesiastical Herald"), which he continued to publish later on in Athens and in New York City.

In 1912–1913 he travelled to Athens where he collaborated with Ion Dragoumis and a commission of the Greek Ministry of Foreign Affairs to explore fundraising for issues which had arisen with the return of territories under the jurisdiction of the Ecumenical Patriarchate to Greece, Serbia, and Bulgaria while drafting a report on the return.

Ιn articles in Ekklisiastiki Kirika in 1914 he would be opposed in every proposal put forward by the metropolitans of the newly-returned territories, for reasons of ethnic politics: they feared the diminution of the Ecumenical Patriarchate, in which he fulfilled the role of ethnarch.