Science and technology-based agencies are increasingly subject to questions of social acceptance. Therefore, they engage in ‘legitimation practices’, which we define as the agencies’ own inside-out practices seeking to ensure legitimacy. Sociological institutionalism suggests that as their formal mandate and overall challenges are comparable, agencies would develop similar practices through isomorphic processes . Likewise, other theories suggest that the agencies’ practices will address specific legitimacy communities of stakeholders. This paper compares the legitimation practices of three European agencies, EFSA, EMA and EPO examining the variation across the institutionalized nature (how) and the concrete issue-framings (what) of those practices. The findings show that the agencies do not develop isomorphic features, and that they issue-frame their practices differently (some more narrow than others). Narrow issue-frames might secure pragmatic legitimacy for the agency, but at the expense of wider normative legitimacy claims which might prove crucial in times of controversy.