IPTRID operates as an independent entity with its own institutional framework, managed by FAO in a manner similar to that of FAO Trust fund projects.

IPTRID governance structure is formed by a Secretariat, a Management Committee and a Consultative Group. In addition, but not as a governance body per se, the ICID-IPTRID Advisory Committee has been supporting the Programme since its inception.

IPTRID Secretariat manages activities on a day-to-day basis, under the supervision of a Programme Manager. The Secretariat tasks are implemented through a team of high-level experts, strongly collaborating with the institutions and resource centres taking part in the IPTRID's Network. From 1998, the Secretariat is located in FAO Headquarters (Rome, Italy).

IPTRID Management Committee (MC) is responsible for overseeing the implementation of the work programme by the Secretariat and for advising the Programme Manager on technical and management actions. The MC Chair is the FAO representative, appointed by the Assistant Director-General of the Agriculture Department of FAO. The MC meets at least twice a year and consists of the following members: one permanent member each from the host organization, the donors and ICID, four members selected from the Network other than ICID and two ex-officio: the Chairperson of the CG and the Programme Manager.

IPTRID Consultative Group (CG) is the highest decision-making body of the Programme, being responsible for providing policy direction, strategy, fund raising and budget approval. It meets at least every 12 months and is composed of a maximum of 22 members, including a chairperson, representatives of funding partners, members of the Network and of developing countries; observers and / or IPTRID Secretariat staff may be invited to attend.

The ICID-IPTRID Advisory Committee guarantees a strong link with ICID, as one of the founders of IPTRID. It advises the CG, MC and the Secretariat on technical aspects of the programme and promote collaboration between IPTRID and the ICID National Committees.