In 1985 he was named Associate General Secretary of the MECC and Director of its Unit on Education and Renewal. The MECC became increasingly involved in Christian-Muslim dialogue under the Rev. Jarjour's leadership.
During his nine-year tenure with the MECC, Jarjour brought the council's program closer to the grass roots of the churches, and rationalized its structure. He maintained the council's ministries despite shrinking financial resources. He also worked to strengthen the ministry of the council among its member churches and especially in the Holy Land. He supported the cause of the Palestinian people, and advocated for the preservation of the Arab identity of Jerusalem.
He has organized and led several events like the Muslim-Christian conference on Jerusalem (Beirut, June 14–17, 1996). Over the years, the council's role as the venue for communication between middle eastern Christians and Muslims was enhanced. Jarjour was among the contributors to and editors of the landmark document of the Arab Working Group for Christian Muslim Dialogue, “Dialogue and Coexistence: An Arab Muslim-Christian Covenant” (finalized in Cairo in December 2001).[full citation needed]
Jarjour was instrumental in planning and administering an important meeting between the heads of the Middle East's churches (Council of Nicosia). Under his administration, the council's relief work in Iraq continued to be effective. The council was also on the ground to respond to the 1997 earthquake in Iran.[10] He administered the program on Justice, Peace and Human Rights which evolved into an effective instrument for analysis, training and promoting the concerns not only of Christians but of all groups in middle eastern society.[citation needed]
Jarjour led the Arab Group for Christian-Muslim Dialogue on activities in the region and internationally,[11][3] which culminated in an important document on Christian Muslim dialogue (The Christian Muslim covenant). He also developed the activities of the World Association for Christian Communication in the Middle East during his time as director.[12][13]