The aim of this paper is to examine if, and to what extent, the EU governance system corresponds to the principles and demands of procedural legitimacy. We analyze procedural legitimacy as this is developed in the work of Lon Fuller and Robert Summers, and we conceptualize and examine legitimacy at the EU level through the three criteria of input, output, and throughput. We use these criteria to analyze the basic rationale and components of the 2015 Better Regulation Agenda of the Juncker Commission, arguing that it has enhanced citizens’ involvement in the policy-making process of the EU and has led to increasing participatory practices, by strengthening throughput legitimacy. However, there are still shortcomings in establishing a deliberative mode of public engagement. Throughput seems to have a considerably increased importance in the EU’s quest for legitimacy, although there is still room for improvement.