There is a blossoming of voluntary certification initiatives for sustainable agro-food products and production processes. With these certification initiatives come traceability in supply chains, to guarantee the sustainability of the products consumed. No systematic analysis exists of traceability systems for sustainability in agro-food supply chains. Hence, the purpose of this article is to analyze the prevalence of four different traceability systems to guarantee sustainability; to identify the factors that determine the kind of traceability systems applied in particular supply chains; and to assess what the emergence of economic and market logics in traceability mean for sustainability. Two conclusions are drawn. Globalizing markets for sustainable agro-food products induces the emergence of book-and-claim traceability systems, but the other three systems (identity preservation, segregation and mass balance) will continue to exist as different factors drive traceability requirements in different supply chains. Secondly, traceability itself is becoming a market driven by economic and market logics, and this may have consequences for sustainability in agro-food supply chains in the future.