The concept of innovation ecosystems brings to light a whole set of stakeholders that face the entire set of barriers to making new technologies change people´s lives. This research aimed to understand and analyze the innovation ecosystem in organic and agroecological production in the Federal District, Brazil, and its directly influenced area. A questionnaire was applied to 27 institutions identified as the backbone of the innovation ecosystem. The Gephi 0.10.1 software and the Force Atlas 2 network algorithm set up the relationship network. We verified a certain misalignment between expected roles and functions performed by 66% of the stakeholders. Low integration and dispersed relationships in the network were observed with a misalignment around the innovation concept in organic food production. This arrangement of the ecosystem is compatible with the initial stage, in which stakeholders and resources would be spread out and demobilized. Although shared governance is the most effective for an innovation ecosystem, the analyzed ecosystem demands centralized governance with a leading organization. Strengthening strategies were proposed to (i) define leadership, (ii) define roles or competencies, and (iii) strengthen community attributes.