Hundreds of firms have pledged to eliminate deforestation from their supply chains. Yet little is known about how supply chain structures interact with the design and implementation of forest-focused supply chain policies (FSPs) to influence their effectiveness and equity. We present a pan-tropical comparative analysis that explores how the design, implementation, and outcomes of FSPs shape, and are shaped by, supply chain structures. We conducted 173 stakeholder interviews and focus groups across four cases involving commodities that account for over half of agriculture-driven tropical deforestation: Brazilian cattle and soy, Indonesian palm oil, and West African cocoa. Drawing on Global Value Chain analysis, we propose an interpretive middle-range theory to connect supply chain structures with FSPs’ outcomes. We find that the governance of deforestation-free production is influenced by the extent of FSP adoption and codification, and producers’ capabilities to comply. These governance factors shape supply chains’ vertical structures (firm–supplier linkages) and horizontal structures (collective market share of firms with FSPs), which in turn shape FSPs’ outcomes. When FSPs are highly codified, producers have high capabilities, and market share is high, firms can implement FSPs through structures involving less explicit coordination. This makes effectiveness–equity synergies more likely. When codification, producers’ capabilities, and market share are low, firms coordinate deforestation-free production directly. This increases control but risks excluding noncompliant producers, while low market share enables leakage. A more transformative approach would therefore see firms collaborating to promote widespread adoption of highly codified FSPs while building producers’ compliance capabilities across their supply bases.