The Baptist tradition is defined in large part by its commitment to congregational church governance. The BFM2000 states that a New Testament church is 'an autonomous local congregation of baptized believers' who govern their own affairs under the lordship of Christ and the authority of Scripture. There is no hierarchical authority above the local congregation — no bishop, synod, or magisterium that can impose doctrinal or policy decisions on a local SBC church.

Scripture alone (sola scriptura) is the supreme and final authority in matters of faith and practice. While the BFM2000 serves as a broadly shared confessional guide, it is described as a 'consensus' document rather than a binding creed. Individual soul competency — the right and responsibility of each person to read and interpret Scripture under the guidance of the Holy Spirit — is a historic Baptist distinctive.

The SBC functions as a voluntary cooperative of autonomous churches. Cooperative Program funding supports missions, seminaries, and social ministries, but participation does not compromise local church independence. The SBC can disfellowship congregations for doctrinal or ethical violations (e.g., approving same-sex unions), but cannot directly govern them.