Soybean peroxidase is an enzyme derived from soybean hulls. Peroxidase has much commercial potential as an ingredient in the manufacturer of polymers and specialty chemicals, as a dough conditioner, and as a component in medical test kits. Commodity soybean cultivars contain various amounts of active peroxidase enzyme. This study evaluates alternative supply chain arrangements for moving soybean hulls containing peroxidase from producer to processor. Results suggest at current peroxidase levels in soybeans, supply chain arrangements involving soybean segregation offer cost advantages over the standard commodity supply chain. In addition, a supply chain involving high peroxidase cultivars may offer enough cost savings over the commodity supply chain to justify full identity preservation of the high peroxidase soybeans from producer to processor.