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Following his graduation he went to Alexandria, Egypt, where he was ordained a [[priest]] and served the Church of Saint Nicholas in Cairo with great distinction. In recognition of his piety and brilliance as a preacher, as well as his administrative ability, he was consecrated Bishop/Metropolitan of Pentapolis (an ancient [[diocese]] in Cyrenaica, in what is now Libya) by the Greek Orthodox Patriarch Sophronios in 1889.

He served as a bishop in Cairo for one year, but was then unjustly removed from his post. This was a result of lies made up by jealous clerics who envied his popularity with the people. Patriarch Sophronios refused to listen to St. Nectarios, who was sent away from Egypt without trial or explanation and was never given an opportunity to defend himself.