MES is a democratic organisation run under the Societies Act. It is headquartered at Calicut. General body in which all members can participate is held once in a year.

There are 4 categories of members.

1. GOLDEN
2. SPECIAL PATRON
3. PATRON
4. LIFE

All members have equal rights. Elections are held every 3 years and an executive of 51 members out of which 11 are office bearers including President, four Vice Presidents, General Secretary and four secretaries and a Treasurer.

All properties are registered in the name of General Secretary. There are no separate trusts for institutions. MES is a de-centralised organisation so that local developments may take better shape, but the final authority is the central committee.

There are 4 tiers of institution.

1. Central institutions
2. Institutions run by District committee
3. Institutions run by Taluk committee
4. Institutions run by Local Committee

The central and other elected committee nominate local management committees to run these institutions .The central committee monitors these institutions, through its instruments like CBSE board, internal audit etc. The central committee also helps the local institutions to get State Government , University and CBSE recognition & affiliation and Central and State aid. Local committees are given maximum autonomy in admissions, appointments etc in these institutions.

The All India MES is promoted by MES Kerala to co-ordinate activities of various Muslim organisations working in the education sphere in India.