The ASCIM is a non-profit organization and has two main organs:
- The General Assembly, organ of manifestation of the social will; and
- The Administrative Council, representing the Assembly when it is not in session.
To coordinate and implement the programs of the ASCIM, a central administration supervises the planned activities. In 2018, the headquarters of the ASCIM moved to Yalve Sanga, a village in the department of Boquerón.
The primary function of the central administration is to coordinate the activities related to the areas of agriculture, education, health and activities in the intercultural, social and spiritual fields. It is also responsible for financial managment, inter-institutional relations and hiring of employees for the institution.