Public demands for accountable, problem-solving, and impactful research, together with global climate and inequality crises, push research organisations to rethink their impact strategies beyond academic performance indicators based on peer-reviewed publications. Part of these organisations conduct applied research and attempt to assess the effect of their activities on the ground. This is the case for agricultural research organisations, which mission is to improve performances of eco-agri-food systems across all sustainability dimensions. Yet, these assessments have mainly remained concentrated along specific research lines and performance indicators, lacking explicit reflection on the theories of change against which the impact of research should be evaluated. They also tend to prioritize quantitative measures, with the traditional question “which benefits from one invested dollar?” and focus on research outputs (such as publications, patents, technologies, events), less often on understanding the uptake of these outputs by stakeholders, the associated behavioral changes they generate, and the mechanisms underlying those changes. This is encouraged by research-funding mechanisms that tend to favor short-term projects, logic-framework exercices, and projects' output rather than behavioral change and impact per se. More in-depth considerations are necessary to examine research through the prism of impact, at both research organisation and wider research ecosystem levels.