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The number and role of agencies in the EU has grown significantly, a process often referred to in the EU legal scholarship as agencification. The trend has intensified since the Lisbon Treaty, which codified agencies as part of the EU’s institutional machinery. A new type of independent EU agency, endowed with considerable powers, has emerged, especially in the energy sector. This article focuses on the agencification phenomenon in the EU energy sector and, more specifically, the delegation of power and the use of institutional margins of discretion in that context. While agencies have a margin of discretion within which they can make decisions that have general application, this discretion should be limited to scientific and technical questions; questions of a political nature should fall outside that margin. From a practical point of view, the challenge is that the divide between what is technical or scientific and what is political is not always clear. The article argues that the delegated rule-making by Agency for the Cooperation of Energy Regulator (ACER) in the EU energy sector stretches the boundaries of the Meroni doctrine by subsuming questions that are not solely technical in nature but may involve political discretion as well.