The Conference of the Parties (COP) is the CMS decision-making body. It meets every three years. Its functions are enumerated in Article VII of the Convention. For example, it reviews the Convention's implementation, adopts budgets, resolutions and recommendations, amends Appendix I and II and decides on priorities for future CMS activities.

The Standing Committee (StC) provides policy and administrative guidance between regular meetings of the COP, particularly on general policy as well as on operational and financial issues. It was created by Resolution 1.1 of the First Meeting of the Conference of the Parties. The StC consists of representatives of the Parties, in particular from each CMS region, the Depositary and a delegate representing the country that plans to host the next meeting of the COP. The StC meets at least annually.

The Scientific Council (ScC) advises the COP and the Secretariat on scientific matters and priorities for research and conservation. Its functions are enumerated in Article VIII of the Convention. The ScC consists of experts appointed by CMS Parties. In addition, the Convention provides for the appointment of a limited number of qualified individuals -appointed councillors- who are recognised experts in their field or region. The ScC presently has 8 appointed councillors whose expertise covers aquatic mammals, African fauna, Asian fauna, birds, bycatch, fish, marine turtles and neotropical fauna. Scientific Councillors participate in ScC meetings in their capacity as experts, not as governmental representatives. The ScC meets once a year.

All three bodies have the possibility to establish working groups on particular species or other topics.