The BAPE is made up of 7 full-time members, including a President and a Vice-President. These members are appointed by the government.

When the Minister of Sustainable Development, Environment and Parks asks the BAPE to hold an inquiry and a public hearing, the President of the BAPE sets up a commission of inquiry and designates the person in charge. The person who chairs the commission is usually a full-time member of the BAPE and is assisted by commissioners chosen based on their expertise in relation to the specific elements and issues of the submitted project. To enable the President to set up commissions in a timely manner and to satisfy the requirements of the mandates entrusted to the BAPE by the Minister of Sustainable Development, Environment and Parks, the President can also resort to a list of part-time members appointed by the government.

Members are required to take an oath, and, while conducting the inquiries entrusted to them, they have the powers and immunity of commissioners appointed under An Act Respecting Public Inquiry Commissions (R.S.Q., c. C-37). As commissioners, they can notably request any document that may be useful in understanding the file. The formal exercise of coercive powers that are officially available to a BAPE commission, is however avoided wherever possible.

The President assumes leadership of the organization. He is assisted by the Vice-President, the assembly of members, the Secretary, the Executive Director of Administration and Communications, and the Director of Environmental Expertise and Coordination.

In their capacity as commissioners, members participate in and conduct the commissions, while ensuring the management of the resources entrusted to them to carry out their mandates.