Free Will Baptists practice congregational polity — each local church is autonomous and governs its own affairs under the lordship of Christ. However, unlike some independent Baptist churches, Free Will Baptists maintain associational connections. Local churches band together in associations (regional groupings), which convene annually and provide pastoral fellowship, doctrinal guidance, and cooperative ministry.

At the associational level, Free Will Baptists resolve disputes, ordain ministers, and provide accountability. Associations can recommend that churches correct doctrinal or moral departures, but they cannot unilaterally impose decisions on autonomous congregations. The National Association of Free Will Baptists is a fellowship of associations and churches, providing broader coordination, theological resources, and missionary cooperation.

Scripture is affirmed as the supreme authority in matters of faith and practice. While the Treatise of the Faith serves as a shared doctrinal statement, it is subordinate to Scripture. Individual conscience and Bible study are valued, consistent with Baptist tradition. The Free Will Baptist emphasis on congregational autonomy is balanced with associational accountability, creating a polity that preserves local freedom while maintaining broader denominational identity and theological standards.