This article explores the rise of new conflicts of sovereignty especially with regard to popular sovereignty in the EU polity. It asks whether referenda in the national realm are effective tools to enhance popular sovereignty at supranational level. To elucidate this question, we distinguish between embedded and unilateral referenda. Empirically, the paper focuses on the referendum called by the Greek government on the proposed Memorandum of Understanding in 2015. While ambiguous from the outset, the referendum turned out to be of an embedded nature and failed to enhance popular sovereignty. Based on elite interviews and analysis of the discussion in the media, our analysis shows that the referendum was envisaged by the Greek government instrumentally to put pressure on the other negotiating parties and tackle internal party disagreements. This turned out to be a self-defeating strategy ignoring the popular mandate and failing to improve the conditions for financial assistance.