He became a specialist in the history of contemporary atheism and subsequently earned a doctorate in canon and civil law at the Pontifical Lateran University.
He worked at the Roman Rota from 1969 until 1972, and represented the Holy See in the Middle East for the Congregation for the Oriental Churches from 1969 to 1993.
On November 11, 1996, Pope John Paul II appointed him as bishop of the Maronite Catholic Eparchy of Saint Maron of Montreal.
Its construction has undergone problems of financing and Monsignor Khoury intervened personally to ensure completion of the project.
On February 28, 2005, Bishop Khoury signed an open letter with local Sunni, Shiite and Druze religious leaders objecting to the amendment in the definition of marriage by then Canadian Prime Minister Paul Martin.