Prior to 2004, each of the Agreement’s Parties determined its own priorities and management projects at a national level. Cooperation with the other Parties was informal and occurred only occasionally, in order to establish shared aims as part of the development of the  pdf Management Plan (French version)  -  pdf Management Plan (Italian version) , which the three countries officially adopted in September 2004.

With the creation of the Permanent Secretariat in 2006, the three Contracting Parties began to routinely work together to implement the provisions of the Management Plan.

The general organization chart for the Pelagos Agreement is laid out as follows: