The Ministerial Council of PERSGA is responsible for setting policies and directions, approving its budget, and establishing technical policies. The council is composed of the ministers responsible for environmental affairs in the member states and convenes every two years at the organization’s headquarters or any other location specified by council regulations or decisions. A preparatory meeting of the focal points is held beforehand to review and draft decisions before presenting them to the council. The council’s presidency rotates among the contracting parties in alphabetical order.

The Secretary-General heads the Secretariat and manages the tasks outlined in the Jeddah Convention, its protocols, annexes, action plans, and the work of the Secretariat according to the council’s resolutions. The Secretariat includes specialized experts who carry out daily operations and coordinate programs with the member states through national focal points.