The IMU is an autonomous church organized at national level, with its own authorities. The General Assembly, which meets every two years, chooses a President, Vice-president and an Executive Advisor that treats the administrative topics and relations with the State, and a National Meeting of Vida and Mission that directs the life and mission during the following period; both bodies are integrated by pastors and laymen.

There are several educational institutions  that are a part of the IMU: in Montevideo, Institute Crandon, Institute of Good Will and the Institute University Methodist Crandon, and in the interior, School and Lyceum Crandon Salto, and social services to the sectors in need.