The MTF is governed by a Steering Committee with three co-chairs, the Office of the Presidential Adviser on the Peace Process, the Bangsamoro Development Agency, and the World Bank. Other members of the Steering Committee are the Mindanao Development Authority and the contributing donors. The United Nations Resident Coordinator and the Japan International Cooperation Agency are invited as observers, as other major development partners for peace and development in Mindanao.

A Technical Management Group (TMG) operates under the Steering Committee to review project concept notes, appraisal packages and other technical documents for endorsement to the Steering Committee. It comprises technical level staff of the three co-chairs and the contributing donors.

A Secretariat staffed by the World Bank supports the Steering Committee and the Technical Management Group. The Secretariat is primarily responsible for coordinating the overall work program of the MTF.