Voluntary commodity standards are widely used to enhance the performance of tropical agro-food chains and to support the welfare and sustainability of smallholder farmers. Different methods and approaches are used to assess the effectiveness and impact of these certification schemes at farm-household, village, cooperative, and regional level. We provide an overview of the results from robust impact studies on coffee, tea, banana, cocoa, and cotton certification programmes. Overall outcomes show rather modest net revenue effects for farmers, small direct income effect for wage workers, and contested sustainability effects. Most impact studies focus on primary sourcing, but devote less attention to changes in trust and governance throughout the value chain. Moreover, implications for gender issues and supply chain trust are not always fully addressed. In order to better understand these somewhat disappointing effects, we discuss different fallacies and drawbacks that affect impact studies concerning commodity certification programmes. Main attention is given to perverse incentives for intensification and specialization that arise from certification. Moreover, spillovers to other (non-certified) farmers and spatial externalities at landscape level may reduce net effects. Important secondary effects related to behavioural change (risk, trust) and local innovation dynamics are usually overlooked. Current practices in value chain development programmes should focus increasingly on dynamic effects of upgrading and improved market integration. New interactive impact assessment approaches (gaming, multi-agency simulation) that address integrated value chain relationships offer promising perspectives for real-time and systematic analysis of alternatives for smallholder value chain inclusion beyond certification.