Drawing on the conceptual framework of intermediations in grassroots innovation for sustainability, this paper presents the first in-depth analysis of the role of third sector organizations in citizen science. The empirical data are derived from 31 case studies of associations (representing 80% of third sector organizations in France). We identify two clusters of associations (social innovation and natural sciences) based on research domain. They differ in epistemic cultures, but they both value experiential and actionable knowledge. We present an analytical framework to characterize the role of these associations in citizen science. Derived from systemic intermediations for transitions, this framework is based on the association’s position in networks, infrastructures, and projects. Our results reveal four categories, three of which are intermediations that depend on the organization’s position in the network, the degree of structuration of its partnerships with academics, and the goals and achievements of the projects in which it is involved. Associations do not only articulate different knowledge in projects, they also contribute to organizational learning in networks. In addition, associations perform the boundary work required to build hybrid infrastructures with institutions. A fourth category unveils the complexity of structuring hybrid epistemic communities for sustainability. This four-way categorization of intermediations highlights the crucial roles of associations in a systemic approach to citizen science.