To function as a regional entity and to conduct research that no one nation can undertake on its own, the IAI was conceived as a network of collaborating research institutions working together to implement the Institute's Science Agenda. Existing resources, including institutions and projects, are fused with IAI driven programs to create new institutional arrangements throughout the region.

The IAI has Four Permanent Organs and a Multinational Network of Research Institutions:

The Conference of the Parties (CoP) : Comprises all countries ratifying the Montevideo Agreement and is the Institute's policymaking organ. It establishes, reviews, and updates the Institute's policies and procedures and evaluates its work.

The Executive Council (EC) : Is composed of nine members, each of whom is elected by the Conference of the Parties for a two-year term, and has two mandates: (1) to develop policy recommendations for submission to and approval by the Conference of the Parties, and (2) to ensure that policies adopted by the Conference of the Parties are implemented by the Directorate.

The Scientific Advisory Committee (SAC) : Is the Institute's main scientific advisory body. It has nine members elected by the Conference of the Parties for a three year term. It makes recommendations to the Conference of the Parties regarding the Science Agenda, long-term plans, the Institutes annual program, science programs to fund. In addition, it assesses the scientific results of the Institutes funded research.

The Directorate : Is the institute's primary administrative organ and is composed of a Director, Scientific Officer, Administrative and Financial Officer, Capacity Building Officer, Information Technology Manager, Program Manager and support staff .

The Multinational Distributed Networks of Research Institutions : The IAI research structure was envisioned to be developed as a distributed network of national and international research and policy institutions working in global change issues in the region. Under the IAI scientific program Collaborative Research Network (CRN), these institutions will develop tools to link existing research groups and to create integrated and coordinated research programs that focus on global change issues of regional importance. Participants in the IAI research network will be determined by a competitive peer review proposal process and subject to periodical reviews of ongoing research programs.