ABSTRACT Upon taking office as President of the European Commission in 2014, Jean-Claude Juncker initiated a series of reforms to the internal workings of the EU executive. Existing research suggests that these have been successful in increasing political steering, creating a Commission which focuses on fewer fields, controls the policy activism of its officials and produces less legislative output. However, much of this research focuses on the Commission as a whole. This article addresses a gap in the literature by exploring how the Juncker reforms have impacted upon the policy-making structures and internal dynamics within two contrasting policy sectors – energy and health. It finds that the reforms have been successful in prioritising selected policy initiatives and increasing top-down steering of the Commission but that, whilst this has led to centralised coordination and reduced conflict in energy policy, it has served to curb purposeful opportunism and legislative activity in health policy.