The highest governing body of CEC is the Assembly, held every 6-7 years and composed of delegates appointed by member churches as well as representatives of associated and partner organisations.
A 40 member Central Committee meets annually to oversee the implemetation of the decisions of the Assembly. A presidium of 10 members serves as executive to the Central Committee.
The structure of CEC consists of a General Secretariat and three Commissions: Churches in Dialogue, Church & Society, and the Churches' Commission for Migrants in Europe. CEC presently has a staff of some 30 persons in three locations: Geneva, Brussels and Strasbourg.