CONTEXT: Digital technologies nowadays play a major role in innovation within the agri-food domain. The evolution of IT systems has currently arrived at a level that involves complex systems integration and business ecosystems in which many stakeholders in different roles are involved. A new paradigm for digital innovation is needed that copes with this increased complexity. OBJECTIVE: This paper presents an empirically informed framework for analysing and designing viable, sustainable digital innovation ecosystems in the agri-food domain. METHODS: The research is based on a series of European large-scale public-private innovation projects from 2011 to 2021 with a total budget of 73 M€. They involved hundreds of stakeholders that were developing a large number of digital solutions through which a digital innovation ecosystem for agri-food was formed. In a longitudinal study, a conceptual framework was used to analyse these projects and describe how the digital innovation ecosystem has developed. Lessons learnt are translated into a number of design principles and an organizational approach to foster digital innovation ecosystems in agri-food. RESULTS AND CONCLUSIONS: The conceptual framework consists of 6 key concepts: (i) innovation strategy, (ii) innovation organization, (iii) innovation network that contains (iv) the innovation process and (v) the innovation object and finally (vi) an innovation infrastructure. Along these 6 concepts, lessons learnt and in total 21 design principles are derived from analysing the projects forming a basis for the organizational framework. At the core of this framework is a lean multi-actor approach to trials and use case development interacting with a set of multidisciplinary activities: (i) developing a common technical collaboration infrastructure, (ii) identifying value streams with user engagement, (iii) engaging the right partners and stakeholders at the right time supported by strategic project planning and dynamic management. The most important conclusion is that effective, successful and quick use of appropriate IT in agri-food requires that actors should not be analysed in isolation from both their technological and business environment. Another consequence is that a ‘minimal viable ecosystem’ only emerges after considerable time, resources and ingenuity is invested and may require outside (government) intervention. SIGNIFICANCE: Results from this paper can be used both by public and private stakeholders to diagnose and improve digital innovation projects and develop viable, sustainable digital innovation ecosystems in agri-food.