The Church of God (Anderson) is distinguished by its rejection of formal ecclesiastical structures and creeds in favor of direct dependence on Scripture and the Holy Spirit. While the church has developed practical cooperative structures for voluntary fellowship and mission, it maintains that these are subordinate to the spiritual unity of all regenerate believers. The invisible church—the body of all true believers regardless of denominational affiliation—is the primary understanding of the church.

Local congregations possess significant autonomy, united with other Church of God congregations through voluntary fellowship and mutual recognition of one another's spiritual authenticity. Leadership is recognized for its spiritual fruits and pastoral gifts rather than through rigid hierarchical appointment. The church's governance emphasizes both local church responsibility and broader connectional support. No central authority beyond Scripture and the fellowship of believers determines doctrine; the church exists to help believers grow in holiness and unity while respecting the sovereignty of the Spirit in leading the church.