Church is managed, in accordance with the statute, by the metropolitan in co-operation with Synod, elected by the EOC MP Council. Presently the members of the Synod are as follows:
- Cornelius, Metropolitan of Tallinn and All Estonia (chairman)
- Bishop Lazar
- Archpriest Oleg Vrona
- Hieromonk Iona (Golovastikov)
- Archpriest Vitaliy Gavrilov
- Archpriest Daniel Lepisk
- Sergy Männik
- Oleg Burdeinyi
Hieromonk Sergy (Telih), Synod's Secretary, is responsible for Synod proceedings.