Visibility, contestation and distrust are key challenges to all parts of the European Union (EU), but they pose particular problems for the Union’s non-majoritarian institutions as they cannot fall back on traditional democratic legitimacy. How do these institutions respond to their politicisation? Building primarily on organisational theory, we conceptualise the responses of the institutions, and develop a set of testable hypotheses on the variation in responses. We illustrate the different arguments using examples from the European Commission, the European Central Bank and EU agencies. Moreover, we present a research agenda for the systematic study of non-majoritarian responses to the politicisation of Europe