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To date, assessments of the sustainability of agricultural commodity supply chains have largely relied on some combination of macro-scale footprint accounts, detailed life-cycle analyses and fine-scale traceability systems. Yet these approaches are limited in their ability to support the sustainability governance of agricultural supply chains, whether because they are intended for coarser-grained analyses, do not identify individual actors, or are too costly to be implemented in a consistent manner for an entire region of production. Here we illustrate some of the advantages of a complementary middle-ground approach that balances detail and scale of supply chain transparency information by combining consistent country-wide data on commodity production at the sub-national (e.g. municipal) level with per shipment customs data to describe trade flows of a given commodity covering all companies and production regions within that country. This approach can support supply chain governance in two key ways. First, enhanced spatial resolution of the production regions that connect to individual supply chains allows for a more accurate consideration of geographic variability in measures of risk and performance that are associated with different production practices. Second, identification of key actors that operate within a specific supply chain, including producers, traders, shippers and consumers can help discriminate coalitions of actors that have shared stake in a particular region, and that together are capable of delivering more cost-effective and coordinated interventions. We illustrate the potential of this approach with examples from Brazil, Indonesia and Colombia. We discuss how transparency information can deepen understanding of the environmental and social impacts of commodity production systems, how benefits are distributed among actors, and some of the trade-offs involved in efforts to improve supply chain sustainability. We then discuss the challenges and opportunities of our approach to strengthen supply chain governance and leverage more effective and fair accountability systems.