Vineyard operates as an apostolic movement: local churches are affiliated relationally through a shared theology and culture but retain significant autonomy. National Vineyard associations (Vineyard USA, Vineyard UK, etc.) provide oversight, accountability, and belonging, but do not exercise coercive authority over local churches. The movement is organized by continent and region through Vineyard International.

Within local churches, Vineyard typically uses a team-based leadership model with a lead pastor and a team of elders. The movement values 'servant leadership' strongly and emphasizes accountability within pastoral teams rather than hierarchical authority. This structure reflects Wimber's suspicion of institutional control and his preference for relational, organic structures.