Seventh Day Baptists practice congregational polity, where authority resides primarily in the local congregation under Christ's headship. Each SDB church is autonomous and self-governing, with the right and responsibility to determine its own doctrine, practice, and leadership. The priesthood of all believers is affirmed, and major decisions are made by the congregation rather than by hierarchical authority.

However, individual congregations maintain voluntary fellowship through the SDB General Conference, which coordinates missionary work, doctrinal education, and mutual support without overriding local church autonomy. The General Conference functions as a cooperative body where churches share resources and wisdom, but ultimate authority remains at the congregational level. This balanced approach reflects the distinctive Baptist commitment to local church autonomy tempered by denominational connection.

The SDB recognizes that congregational polity does not mean isolation or individualism. Churches are called to consult with denominational leadership and to consider broader SDB wisdom and practice, while retaining the final authority to govern themselves according to Scripture as they understand it.