In its evaluation cycle, the European Commission emphasises the importance of good data and the systematic involvement of a plurality of policy stakeholders, including citizens. Findings from European Union policy evaluation should inform further law-making, encourage learning and provide accountability. Transparent and inclusive formal procedures and tools are seen as essential for securing citizen participation in risk regulation; however, the Commission faces numerous challenges in securing engagement, particularly concerning the complexity of policy issues and the formal procedures for institutionalised consultations. Considering the Commission’s work from a proceduralist perspective, the article engages with Vivien Schmidt’s notion of “throughput legitimacy” to explore recent procedural innovations emerging since the Better Regulation agenda that have sought to enhance accountability, transparency, inclusiveness and openness, ensuring fairer and more balanced input on EU policy performance. The article argues in favour of greater throughput legitimacy in ex post policy evaluation but recognises challenges to the promotion of evaluation tools and their use by citizens.