The organization is managed by the MCGI Central Administration under the MCGI Workers Ministry.
The Members Church of God International in the Philippines rooted from a similar denomination, the Iglesia ng Dios kay Kristo Hesus, Haligi at Suhay ng Katotohanan (Church of God in Christ Jesus, Pillar and Support of the Truth) which was first led by Brother Nicolas Antiporda Perez in Pulilan, Bulacan, Philippines in 1928.
On December 10, 1936, the Church was registered with the Philippine government by Brother Nicolas Antiporda Perez as first church Presiding Minister with a Central Office in Natividad St., Pasay, Rizal (now Pasay City).
In 2008, Bible Expositions were conducted in the continent of Oceania bringing forth the first congregation in Papua New Guinea.
In the same year, congregations were established in Ghana, West Africa as a result of a series of Bible studies in Africa.