This article explores the impact that the rise of a new, European Council-dominated Union has had for role of EU institutions in the most important issues of the past decade. Building on rational institutionalist theories of leadership, we first develop a New Institutionalist Leadership model that helps us understand the political leadership tasks performed by the European Council and the instrumental leadership tasks that are informally delegated to EU institutions, who then deliver them in the ‘the machine room’ where broad political guidelines are translated into actual binding reforms. The article then traces the empirical evolution of New Institutionalist Leadership in two parallel processes: dealing with concrete reforms such as the Fiscal Compact, and in managing the longer-term reform agenda in what became termed the Leaders’ Agenda. Our findings point to the need for EU scholars to pay closer attention to what is going on beneath the headline-dominating activities of the European Council.