The Alliance has a flexible structure of nine autonomous regions coordinated and supported by a Technical Secretariat. The membership of the Alliance, made up of indigenous and tribal peoples organisations in regional networks, is the highest policy-making body in the network. Policy is formulated through the Alliance's International Conferences, which have been held every two to three years since the establishment of the Alliance in 1992. The most recent was in Nairobi, Kenya, in November 2002.

Between these assemblies, the Alliance is coordinated by an International Coordinating Committee (ICC), which meets at least twice a year to monitor the work of the Alliance. The Committee is constituted of 9 Regional Coordinators. Supported by a regional secretariat and the International Technical Secretariat, each Regional Coordinator represents one of the nine regions falling within the Alliance's remit.