The functions of the supervisory board at the IOS are performed by the Scientific Board (SB). SB of IOS makes decisions upon strategic research directions, approves budgets and elects the Management Board of the IOS. Members of SB are elected by the General Assembly of IOS.

Executive power is granted to the director of the Latvian Institute of Organic Synthesis. The Director is elected by the Scientific Board. The duties of the Director are defined by the Law on Scientific Activity. The Director of the IOS and his deputies are the Management Board of the Institute.