Broadening citizen participation in biodiversity governance is often presented as a priority by public institutions. Citizens’ engagement in policy design fostering the protection of biodiversity would indeed allow two-way knowledge transfers between expert knowledge and local knowledge; it would also enable citizens to influence collective choices; and it would finally lead to inclusive decision-making processes. However, the achievement of these promises depends strongly on the capacity of public participation exercises to be fair and efficient. By focusing on these two concepts, this paper aims to contribute to identifying obstacles and tools for public participation in biodiversity governance through a comparative analysis of two case studies. The first one consists of three one-day open space technology meetings, which aimed to engage citizens in orienting biodiversity research during Paris COP21. The second one was a two-year long experiment of Citizens Committees-based participatory governance led by the French Office for Biodiversity. These two case studies are representative of two complementary dimensions of biodiversity governance: the orientation of scientific research and the regulation of individual and collective actions through laws, rules and institutional communication. Among other insights, our results determine the existence of strong skepticism regarding the political outputs of public participation, which is reinforced when the objectives and the means of the exercises are not clear enough. Second, we argue that the efficiency of participative biodiversity governance depends on the capacity of institutions to propose diversity of citizen engagement formats and objectives in order to reflect the diversity of citizens’ motivations and preferences.