Our roots can be traced back to the early Evangelical Christians that came to the Philippines in 1898. American Baptist Missionary Union began working in Panay and Ilo-ilo Islands and founded Central Philippine University, Baptist Center Church, and Iloilo Mission Hospital in years 1905 to 1907.

In 1928, Dr. Raphael Thomas, a former missionary for the American Baptist Foreign Missions Society (previously the American Baptist Missionary Union), and one of the pioneers of the Association of Baptists for World Evangelism (ABWE) established the First Baptist Church of Manila in Padre Faura Streets. In 1956, the FBCM ordained Rev. Antonio F. Ormeo as her first Filipino pastor.

FBCM moved to Project 6, Quezon City, in a temporary structure in 1973, where it is now located. By the grace of God, the FBCM was able to construct and dedicate a three-story structure in 1981 with the aid of our brethren in Singapore. During this period, work also began on the four-story church structure.

After 32 years of especially challenging but successful ministering in the church, Rev. Antonio F. Ormeo made the decision to retire in 1987 due to his old age. In 1987, FBCM welcomed Rev. Ebenezer T. Nacita as her interim senior pastor and eventually, as her Senior Pastor in 1989. Pastor Nacita is now serving as a pastoral staff member at FBCM after stepping down as Senior Pastor of the church in the year 2022.

Over the years, FBCM has helped several churches with pastoral training, counseling, and rehabilitation, church planting, supporting both local and international missionaries, running bible institutes, and equipping churches to be self-sufficient, self-propagating, and self-managing.