From 1955 to 1975 he taught Arabic literature, French literature and humanities (Classical Greek and Latin) at the Seminary of St. Paul, Harissa, Lebanon. Then he taught philosophy, sociology and patristics at St. Anne of Jerusalem (Salahiyeh). He finally returned to Lebanon to teach theology, liturgy and Islamology at St. Paul's High Institute, Harissa.
From 1975 to 1987 he was superior general of St. Paul's Society. He was consecrated bishop of Melkite Greek Catholic Eparchy of Nossa Senhora do Paraíso em São Paulo, Brazil, on 29 June 1990. In 1998, the Melkite Synod elected him Archbishop of Galilee. He resigned on 10 May 2003 due to his age.
He is active in seeking interfaith reconciliation and for championing the rights of Palestinians. He also currently sits on the Board of World Religious Leaders for the Elijah Interfaith Institute.
His election as archbishop of Galilee was actively opposed by the government of Israel, who said that he favours the Palestine Liberation Organization, resulting in a row between the Holy See and the government of Prime Minister Benjamin Netanyahu. The Holy See noted that selection of a bishop was matter reserved for the Church, "free of all external pressure," and that the Fundamental Accord between the Holy See and the State of Israel "provides for the autonomy of Church and State, each one in its own area." Sources close to Netanyahu said that he wanted to make a "courteous persuasion" in favour of the competing candidate after the PLO began to insistently intervene in favour of Mouallem.
- المطران بطرس المعلّم: من وحي "الربيع" - Bishop Boutros Mouallem: Inspirations from the "Spring" 2012
- The Elijah Interfaith Institute - Christian Members of the Board of World Religious Leaders
- Vatican Rebukes Israel Over Comments On Palestinian Bishop. Catholic World News. 7 August 1998.
- Israeli Prime Minister Challenges Pope on Appointment of Bishop Archived 6 February 2005 at the Wayback Machine. Zenit, 8 August 1998. Retrieved May 2007
- Solheim, James (23 October 2002). Christian Leaders from Jerusalem Blocked From Attending Interfaith Meeting in London. Episcopal News Service.