Reformed Baptists hold a congregational form of church governance combined with a Presbyterian structure of elders. The local congregation is the primary locus of church authority, not a denominational hierarchy or individual pastor. Each congregation is autonomous and subject directly to Christ as head, yet accountable to Scripture and associated congregations through voluntary bonds of fellowship. Congregational polity reflects the Reformed Baptist conviction that the church consists of regenerate believers, not infants, and that membership decisions and discipline should rest with the gathered congregation.

Church leadership comprises a plurality of qualified male elders (also called pastors or overseers) and deacons, as outlined in Scripture and elaborated in the 1689 Confession. Elders shepherd the flock, preach and teach, oversee worship and sacraments, and lead in doctrinal matters. Deacons serve the physical and material needs of the congregation. The regulative principle of worship holds that worship practices must be commanded or clearly exemplified in Scripture; whatever is not commanded or derived from Scripture is forbidden.

Authority in the church is ultimately derived from Scripture alone (sola scriptura), not from human tradition, ecclesiastical hierarchy, or individual conscience. The 1689 Confession, while honored as a subordinate standard, is subordinate to the Word of God. Congregational decisions are made through prayer, discernment, and the teaching of Scripture, with the elders providing spiritual leadership and the congregation ratifying major decisions.