There is a paradox between the constant increase of knowledge production in ecology and the limited impact of innovations aiming to improve agro-ecosystems’ sustainability. Drawing on recent design theories’ formalism, this paper shows how shifting from a ‘decision’ pathway (i.e., identify optimal decisions to implement within a set of pre-defined options) to a ‘design’ pathway (i.e., enlarge the range of decision alternatives) may help overcoming this paradox. Considering that the former pathway tends to set off conflicts between stakeholders, inefficient public spending and limited innovation, we propose a conceptual framework facilitating the mobilization of ecological knowledge in innovative design processes. The elaboration of the framework draws upon a three-year collaboration between a design scientist and a research team in ecology which is conducing a long-term research program on reconciling intensive crop production and biodiversity preservation in western France. The framework was then applied to two other contrasted empirical cases, wet grasslands and subalpine grasslands, to reveal its potential in various contexts. The framework proposed is the following: once ecologists identify a key regulation process to be maintained in the agro-ecosystem, which we name “key underlying property”, various configurations of the agro-ecosystem can be explored to meet this property. We introduce the notion of “ecological fund”, i.e., the subsystem in which the key underlying property needs to be maintained, and suggest that it can be the departure point of a design process. An ecological fund is identified on the basis of ecological knowledge, but it guides a design process that may involve various stakeholders, instead of proposing a turnkey solution. We thus show that, despite ecology is often considered either as a discipline of expertise, used to inform decision-making processes, or as a constraint for agricultural production, it provides key knowledge that opens innovative design opportunities for enhancing agro-ecosystems’ sustainability.