Over the years there have been global news reports of ‘bio-piracy’ by companies accused of marketing blockbuster products derived from the biological resources of developing countries. This perception stimulated the adoption of the 2010 Nagoya Protocol, to implement the objective of the 1992 Convention on Biological Diversity that benefits arising out of R&D on genetic resources should be fairly shared with the country of origin. Since October 2014, strict rules apply in the European Union to enforce compliance with the Nagoya Protocol. However, it would be wrong to assume that the new EU Regulation only encompasses bio-prospecting or ethno-pharmacological R&D. Instead, the EU has purposely set up a broad regime that affects companies developing pharmaceuticals, cosmetics and biocides, as well as food, feed, beverages, and any of their components. This article summarizes the new EU Nagoya compliance regime, with examples drawn from the food sector to explain its impact.