The Great Assembly of the Synod is the decision-making institution of the Malagasy Lutheran Church. Its members meet once every four years. The Malagasy Lutheran Church is organised in 23 Regional Synods.
The second level of structure is the Synod Committee which meets twice a year, in May and in November and works according to the decision of the Great Assembly.
The Head Office, as the third level, is the executive body. It is constituted of the President, the Vice President, the General Secretary, the Vice-General Secretary and the Treasurer of the MLC.