By definition, non-denominational evangelical churches operate without a denominational hierarchy above the local congregation. Authority structures and governance models vary significantly: some churches use elder-led governance, others are pastor-led, and some have more congregational models. There is no bishop, synod, or general assembly that has binding authority over independent non-denominational congregations.

Scripture is universally affirmed as the supreme authority for Christian faith and practice. Beyond this, non-denominational churches exercise considerable freedom in how they structure leadership, accountability, and decision-making. The rise of 'multi-site' non-denominational megachurches has introduced a form of network authority in which the founding or senior pastor's vision and leadership shapes multiple campuses without formal denominational accountability structures.

Critics within and outside the non-denominational evangelical world have raised concerns about accountability gaps, the concentration of authority in charismatic senior pastors, and the lack of doctrinal oversight mechanisms. Some non-denominational churches have responded by voluntarily affiliating with loose networks (e.g., Acts 29, the Gospel Coalition) that provide peer accountability and doctrinal resources without functioning as a formal denomination.