EAWLS has a Board of Trustees that acts as its legal guardian.

Otherwise the Society is a membership-based organisation, with members exercising their wishes through the AGM. The AGM elects a Council, consisting of a Chairman, Treasurer and 10 members to oversee the work of the Secretariat that runs the Society. The Executive Director acts as the Council’s Secretary. The Council has established two committees to manage editorial responsibilities for the Society. These are the:
• Swara Editorial Board: This committee assists and advises the editor on the direction and content of the magazine, potential sources of stories (material) and generally provides support in managing the magazine affairs.
• The African Journal of Ecology Editorial Board: This committee collects and edits ecological articles from scientists all over Africa.

The Executive Director heads the Secretariat, which has the following departments (organogram at bottom):
• Conservation Programmes Department: To sustain field work by initiating projects based on pertinent conservation issues facing the East African region.  Within this Department, the Society runs the Coastal and Marine programme and provides the Secretariat for the Kenya Forests Working Group and the Wetlands Forum. The Society will soon be hosting a Conservation Working Group Secretariat to deal with wildlife related issues currently not addressed by existing forums.
• Communication Department: To increase and sustain the number of members of the Society and to keep the members of the Society informed of wildlife and conservation related news and developments through production of Swara Magazine, the EAWLS Newsletter, website and through other fora
• Advocacy Support Unit: This unit is not yet in place.  However during the next few months, we are planning to create it.  The intention is to have a unit that can assist with research and investigation into environmental issues that need an advocacy approach and help develop better governance.
• Administrative Department: To provide, co-ordinate and facilitate quality services to all other departments by ensuring a conducive working environment.
• Finance Department: To provide effective and sound financial and accounting services to the Society