The German Energy Transition is one of the most important and largest infrastructure projects and one of the most significant challenges to German policy‐making. Empirical studies provide evidence for the notion that participation in the decision making process shapes local acceptance of renewable energy technology expansion. In the context of the German Energy Transition, the emphasis on participation in decision making processes seems to involve a paradox. Many different participatory measures have been implemented but many renewable energy projects do not reach a decent level of acceptability. In utilizing the concept of throughput legitimacy, we show that a major threat to legitimacy lies in the incoherent way conventional and unconventional forms of citizen participation are implemented at different scales. According to our analysis, the main challenges are to enable multi‐level participation and to transfer deliberative outcome to the representative system. In referring to innovative democratic procedures in Brazil, we present characteristics and features of participatory measures that may solve these challenges.