Food supply chains complexity present a real challenge to perform economic evaluation of food traceability systems and their innovation/upgrades. In order to perform a supply chain wide economic evaluation a conceptual framework is developed using food traceability reference models. Reference models allow interaction with chain members’ requirements that come from legal and/or customer sources. The paper demonstrates how the requirements will have a definite effect on the costs and design of food traceability systems through the resources they demand. Even though this is a first step into addressing the challenge, more investigation is needed to clarify the boundaries of the two requirements and their economic effects on food traceability systems and their innovations/upgrades.