The programme is implemented through a number of institutional partnerships, guided by the European Union (EU), the Organization of Africa, Caribbean and Pacific States Secretariat (OACPS). 

The African Union Commission (AUC) serves as the regional hub for Africa while the Secretariat to the Pacific Regional Environment Programme (SPREP) and the Caribbean Community Secretariat (CARICOM) serves as regional hubs for the Pacific and the Caribbean respectively.

Activities in support of MEAs are implemented in collaboration with relevant Secretariats of MEAs such as the Secretariat to the Convention on Biological Diversity (CBD), the Secretariat to Convention on Migratory Species (CMS), the Secretariat to the Convention on International Trade in Endangered Species (CITES), Secretariat to the Minamata Convention, Secretariat to the Basel, Rotterdam and Stockholm conventions (BRS) and others. 

In addition, the programme also works with Regional Seas conventions such as the Cartagena Convention, the Abidjan Convention, the Nairobi Convention and the Noumea Convention. 

Institutions like the European Environment Bureau (EEB) also support implementation of the programme.