EAMCEF is governed by an autonomous, multi-sector 9-member Board of Trustees (BOT) representing the Central Government (2), Local Communities (2), Legal Community (1), Academia/Research Community (1), National NGOs (1), International NGOs (1), and Private Sector/Business community (1). Headed by a Chairperson elected from amongst the Trustees, the Board of Trustees (BOT) is the highest policy and decision-making body of EAMCEF. The Trustees hold all land, monies and other properties of the Endowment Fund UPON TRUST and apply the same in accordance with the aims and objectives of the Trust for the benefit of present and future generations. The Board of Trustees governs the Trust and oversees its business in accordance with the provisions of the Trust Deed upon which it was established. The EAMCEF Executive Director serves as Secretary of the Board of Trustees.

The Endowment Fund Secretariat is comprised of the Executive Director, a Conservation Programme Officer (CPO), Marketing and Engagement Officer (MEO), a Finance and Administration Officer (FAO), four Technical and Administrative Assistants, two Field Project Officers (FPOs) and nine Support Staff. The day-to-day activities and operations are undertaken by the Endowment Fund Secretariat based in Morogoro Municipality, headed by an Executive Director and comprised of both professional and administrative staff working with and through partners. EAMCEF effectively collaborates and works closely with various Development Partners, Field Partners, Local Advisory Committees (LACs), Technical/Management Advisors and Local Communities.