In the course of its work, JIU involves many different partners, including its participating organizations, Member States, other United Nations, oversight and coordination bodies, as well as other specialized agencies, international organizations, and non-governmental organizations, as deemed relevant for the conduct of JIU evaluation, inspection and investigation projects.

As stated by the General Assembly, the impact of JIU on the cost effectiveness of activities within the United Nations system is a shared responsibility of the Member States, the Unit and the secretariats of the participating organizations. The acceptance and implementation of JIU recommendations, which could be addressed to as many as 28 different organizations, often require lengthy follow-up efforts and legislative body action.

JIU also coordinates its work with other United Nations system oversight and coordination bodies. It works in contact with the United Nations System Chief Executives Board for Coordination (CEB) Secretariat; the Chairpersons of its High-Level Committee on Management (HLCM) and High-Level Committee on Programmes (HLCP); the Advisory Committee on Administrative and Budgetary Questions (ACABQ); and the Committee for Programme and Coordination of the United Nations (CPC).