PERSGA is an intergovernmental organization governed by a council including ministers handling environmental affairs in each of the seven PERSGA member state. The council meets every two years to approve technical and financial policies.

The organization’s daily affairs are managed by a secretariat run by a team of professionals recruited from various countries in the region and headed by the Secretary General. The kingdom of Saudi Arabia hosts PERSGA Secretariat and its headquarters in Jeddah, since it was established in 1995.

PERSGA has devised a systems of monitoring and evaluation to ensure the Organization is achieving its programme objectives laid out in the Strategic Action Plan, and to incorporate a system of transparency into project management