The first Baptist church in what was then the territory of Alabama was the Flint River Baptist church founded by twelve people on October 2, 1808, at the house of James Deaton a few miles to the north of Huntsville (now known as the Flint River Primitive Baptist Church  ).    The pastor was John Nicholson. Prior to that there had been several Baptist preachers in the territory, including John Canterbery and Zadock Baker. Several more churches were founded over the next few years.  The second Baptist church was founded on June 3, 1809,  originally named West Fork of Flint River Church, although renamed to Enon Baptist Church shortly thereafter.  (In 1861 the Enon church moved to Huntsville, and was renamed the First Baptist Church of Huntsville in 1895. ) John Canterbery was the church's first pastor, called on August 5, 1809. 
The Flint River Association, the first and oldest association of Alabama Baptists, was founded on September 26, 1814.  Flint River Baptist Church  and Enon Baptist Church were charter members.  Initially, several of the FRA's members were churches from Tennessee.  The Flint River Association is still in existence today, consisting of three Huntsville area Primitive Baptist Churches, Briar Fork Church, Hurricane Church, and Flint River Church.  The first church in the southern part of the state was Bassett Creek church, founded by J. Courtney in 1810. By 1820 there were 50 Baptist churches in the state; in 1821, there were 70. Numbers continued to grow in subsequent years, with 6 Baptist Associations and 128 churches in 1825; 250 churches in 1833; 333 churches in 1836; and 500 churches and 30 associations in 1840. 
The geography of the state in the 19th century, with highly different political and economic groups physically isolated from one another by poor transport and communication links, resulted in several Baptist conventions emerging. The most well known, and largest, was the Alabama Baptist Convention founded in 1823 near Greensboro. Members of Siloam Baptist Church in Marion and the Alabama Baptist Convention founded Judson College in 1838 and Howard College, later renamed Samford University, in 1841. But there were others. The General Association of Middle Tennessee and North Alabama was founded in 1841, the East Alabama Baptist Convention in 1856, and the General Association of South Eastern Alabama after the U.S. Civil War. 
Not allowed to be part of the Alabama Baptist Convention during that time, African American Baptists had their own conventions, separate from the white organizations. The Alabama Colored Baptist State Convention, which changed its name in 1974 to the Alabama Missionary Baptist State Convention, was founded in 1868 in Montgomery and by the turn of the 21st century comprised over 1000 churches. In 1898, the New Era Progressive Baptist State Convention split from the ACBSC, and another split in 1920 spawned the New Era Baptist State Convention. The Progressive National Baptist Convention, the fourth of the four major conventions in the late 20th and early 21st centuries, was formed in 1961 after disputes over leadership at the National Convention and over civil rights. 
Much of this history is recorded in the library of Samford University. Baptists are the largest denomination in Alabama, and the University records include full minutes of congregational meetings throughout the state, the personal papers of many Baptist churchmen, and all issues of the Baptist newspaper, The Alabama Baptist from 1835 onwards. 
- William Cathcart (1881). "Alabama Baptists, History of". The Baptist Encyclopedia. Baptist History Series. 1 (reprinted by The Baptist Standard Bearer, Inc. 2001 ed.). Philadelphia: Louis H. Everts. pp. 14–15. ISBN 978-1-57978-909-1.
- Wayne Flynt (1998). Alabama Baptists: Southern Baptists in the heart of Dixie. Religion and American culture. University of Alabama Press. pp. xix. ISBN 978-0-8173-0927-5.
- Alice Eichholz (2004). Red book: American state, county & town sources (3rd ed.). Ancestry Publishing. p. 26. ISBN 978-1-59331-166-7.
- C. Laura; C. Sara; M. Hugh; M. Jack (2006). Alabama Historical Association Markers (2nd ed.). Jack Hood. p. 163. ISBN 978-1-4259-2186-6.
- Hosea Holcombe (1840). A History Of The Rise And Progress Of Baptists In Alabama. Philadelphia: King and Baird Printers. pp. 108.
- Minutes of the Flint River Association, 2009
- Wayne Flynt (1998). Alabama Baptists: Southern Baptists in the heart of Dixie. Religion and American culture. University of Alabama Press. p. 61. ISBN 978-0-8173-0927-5.
- Wayne Flynt (2004). Alabama in the twentieth century. University of Alabama Press. p. 459. ISBN 978-0-8173-1430-9.
- Wayne Flynt (Winter 1969). "Dissent in Zion: Alabama Baptists and Social Issues, 1900–1914". Journal of Southern History. 35: 523–542.
- Daniel L. Cloyd (1978). "Prelude to Reform: Political, Economic and Social Thought of Alabama Baptists, 1877–1890". Alabama Review. 31: 48–64.
- Hosea Holcombe (1840). A history of the rise and progress of the Baptists in Alabama. Philadelphia: King and Baird.
- Wilson Fallin Jr. (2007-07-17). "Black Baptists in Alabama". The Encyclopedia of Alabama. Auburn University.
- Wayne Flynt (2008-11-10). "Southern Baptists in Alabama". The Encyclopedia of Alabama. Auburn University.
- Charles Octavius Boothe (1895). The Cyclopedia of the Colored Baptists of Alabama: Their Leaders and their Work. Birmingham: Alabama Publishing Company.
- Wilson Fallin Jr (2007). Uplifting the People: Three Centuries of Black Baptists in Alabama. Tuscaloosa: University of Alabama Press. ISBN 978-0-8173-1569-6.
- Wayne Flynt (2004). "What would Jesus do? Religion". Alabama in the twentieth century. University of Alabama Press. ISBN 978-0-8173-1430-9.
- Nathaniel Stevenson Reid (1949). History of Colored Baptists in Alabama. Gladsen Alabama.