First Baptist Church was founded by eighteen members in 1867 as the First Freewill Baptist Church. In 1910, it merged with the Missionary Baptist Church of Spencer, and in 1911 attempted to incorporate as the Free Baptist Church, but due to a clerical error in Des Moines (!) was officially named First Baptist Church. At the time of its incorporation it was a member of the Sioux Valley Association of Regular Baptists, a subdivision of the Northern Baptist Convention, later called the American Baptist Convention.

In 1952 First Baptist severed its ties with the American Baptists, voting to become "free, independent, autonomous, and democratic, with allegiance and responsibility to no person or organization but to God." First Baptist has from its founding been a Bible-believing, Gospel preaching, missionary sending congregation.

For 150 years the church has demonstrated the capacity to be used powerfully by God to influence the Spencer area. The people of First Baptist are a loving, caring family that looks out for one another. The church government is organized around three key groups: the Deacon Board, the Trustee Board, and the Mission Committee. The Mission Committee administers its own budget in support of Missions. A Christian Education committee oversees Sunday School and AWANA ministries. The church has a strong history of and commitment to congregational government.