AMCEN and its organs are organised as follows:
The Conference: African ministers responsible for environmental issues are members of AMCEN. They meet every second year and make decisions on environmental issues, including the biennial work programme of AMCEN. Special Sessions of the Conference are held as necessary.
The Bureau: The Conference elects a bureau to serve for a two year period. The Bureau consists of five members (one president, three vice-presidents and one rapporteur) that represent the five sub-regions of Africa . The AMCEN Bureau meets at least twice a year. The role of the Bureau is to provide guidance for the implementation of the decisions of the Conference; assess progress made and actions needed for the effective implementation of the decisions of the Conference; give strategic directions to the Inter-sessional Committee, the Inter-Agency Technical Committee and the Secretariat.
The Secretariat of the Conference is hosted by UNEP's Regional Office for Africa. The main tasks of the Secretariat are to assist the President of the Conference and its Bureau in the implementation of the decisions adopted by the Conference; undertake the organisation of work between sessions; and provide secretariat services to AMCEN, its Bureau and other AMCEN organs during their sessions.
The Inter-Agency Technical Committee comprises representatives from the African Union, the UN Economic Commission for Africa, the African Development Bank, African sub regional organisations and economic groupings; specialised agencies, programmes and organs of relevant UN system, including secretariats of multilateral environmental agreements; specialised non-governmental organisations, private sector, and civil society. The Committee supports the Secretariat to achieve a higher level of co-ordination and integration of activities.