As a crisis of unprecedented speed, pervasiveness, and multi-dimensionality, Covid-19 generated a number of tensions at the intersection of scientific knowledge, information, and political trust. These, on the one hand, played a key role in structuring the politics of the pandemic in Europe. On the other hand, they highlight important challenges in the broader debate on whether and how to restructure liberal-democratic governance for the post-pandemic. Building on this premise, the paper presents the proceedings and results of an innovative two-level mini-public experiment run between June 2023 and March 2024, in which citizens of five European countries—France, Germany, Italy, the Netherlands and Poland—gathered first nationally, and then transnationally, to reflect and deliberate on four issues: 1) the quality of information and disinformation on the pandemic; 2) the production and communication of scientific knowledge on Covid-19; 3) the role of unelected experts in policy-making; 4) the impact of all the foregoing on political trust. The mini-public experiment is a first of its kind, which will be of interest to scholars and policy-makers alike not only for the substantive recommendations it produced, but also for its novel way of aggregating deliberation at different levels, which may provide a model for future citizen consultation within the European Union.