The objective of this article is to draw attention to legitimacy concerns raised by tendencies in EU risk regulation to supplement legislation with alternative regulatory options that are commonly captured under the umbrella term of new governance'. To this end, the risk regulation of nanotechnologies in food serves as an empirical test case. The rise of nanotechnologies affects various societal actors and constitutes a highly controversial development due to the persistence of scientific uncertainties. To reach a compromise in the legislative process is, given the contradicting knowledge claims, a contentious and time-consuming undertaking. This article, hence, shows that controversial decisions are not necessarily taken through the legislaturethe European Parliament and the Councilbut are settled, outside the political arena, in guidance documents or via non-legislative acts. This article argues, relying on an understanding of legitimacy borrowed from Habermas and Scharpf, that despite new governance' ambitions in this direction the legitimacy of these measures is at best controversial.