With the National Council's approval, the President appoints a Secretary General (Sekretera Jeneraly) to manage the day-to-day affairs of the church.
The eight branches (sampana) of the church: Women (Dorkasy), Men (SLK), Youth (STK), Laity (SFL, including the Lay Training School, SEFALA), Sunday School (Sekoly Alahady), Boy and Girl Scouts (SAMPATI), Blue Cross (Vokovoko Manga, which fights drug and alcohol abuse), and Revival (SAFIF, which includes the network of spiritual healing and retreat centres); 3.
The work (asa) of the church, including such diverse initiatives as TOPAZA orphanage, an order of nuns (Mamre), social workers and a chaplaincy program.
The Department of Schools also operates a Teacher Training College that is being incorporated into the newly established Reformed University of Madagascar, which it is working to develop.
The Department of Finance and Human Resources oversees the day-to-day administration of the church, including personnel and fiscal issues.
It also oversees a cheese-making business (FIVATSY), a printing press, a bookstore, and the FJKM property unit (FIFA).
These include the communications unit (AFIFAB) which administers the church's print and broadcast media; the Fruits, Vegetables, and Environmental Education Project (MFEE); and the FJKM Development Department (SAF).
There is a small but significant (7%) Muslim presence, but the bulk of non-Christians practice traditional beliefs that include the veneration of ancestors.
It also has a long history of partnership with the Lutheran Church through the Federation of Protestant Churches in Madagascar (Fiombonan’ny Fiangonana Protestanta Malagasy or FFPM), which operates a number of joint projects, including several schools, Akany Fifampandrosoana and the Akany Avoko Children's Home.