The highest body of non-profit association BirdLife Estonia is the annual general meeting of its members.
The board of Birdlife Estonia consists of one to three members chosen by the council for a period of three years. The council is selected at the yearly meeting of Birdlife Estonia for a three-year term, and consists of 11-20 members.
Chairman of the board is Kaarel Võhandu (kaarel.vohandu@eoy.ee).
Members of the council (2024): Leho Luigujõe (chairman), Elle-Mari Talivee (vice-chairman), Art Villem Adojaan, Andres Kalamees, Mati Kose, Eerik Leibak, Olev Lüütsepp, Pelle Mellov, Urmas Talivee, Aarne Tuule, Tarvo Valker, Peep Veedla.