The MECC initially had three co-presidents, representing each of the Christian "families", becoming four after the Catholic Churches joined in 1990.
The first General Secretary of the MECC from 1974 to 1977 was Rev. Albert Istero. He was succeeded by Gabriel Habib, from 1977 to 1994. In November 1994, Rev. Dr. Riad Jarjour was elected General Secretary. He was replaced after two terms by Guirgis Saleh, a Coptic Orthodox theologian and professor, at the Eighth General Assembly in 2003.