The sustainable development of agricultural systems is currently challenged by many complex agro-environmental issues. These are characterized by an incomplete understanding of the situation and the problems that arise, and the conflicting opinions that result, issues over boundaries that are often difficult to define, and controversy over the multiple goals and uncertain outcomes. Added to these characteristics, we also have the slow and often inadequate uptake and implementation of research outcomes in this complex, real world. In order to improve sustainability of agro-ecosystems, agronomic research must move away from the linear research approaches and extension practices adopted so far that have focused purely on biophysical agro ecosystems. The theoretical operational space of agronomic research must be transformed by considering agronomic issues as part of a broader social-agro-ecosystem. One aspect of this transformation is the inclusion of knowledge collected on a local level with the participation of farmers on the ground. The integration of local experiential knowledge with traditional agronomic research is by necessity based on the participation of many different stakeholders and there can be no single blueprint for how best to develop and use the input received. However, agronomists and policy advisors require general guidelines drawn up from actual experience in order to accelerate positive agronomic change. We address this need through a comparative analysis of two case studies; one involves multi-stakeholder research in a cropping system in the dairy district of Arborea, Sardinia, Italy. The central question was: How can high crop production be maintained while also achieving the EU target water quality and minimizing the production costs? The second case is a multi-stakeholder soil health project from south-eastern Australia. Here the central question was: How can soil decline be prevented and reversed in this district, and soils made more resilient to future challenges? The Social Learning for the Integrated Management and sustainable use of water (SLIM) framework, a useful heuristic tool for exploring the dynamics of transformational change, guided the analysis of the case studies. Within this framework, a key indicator of success is the emergence of new knowledge from the creation of new spaces for learning between researchers and local stakeholders. The Italian case study appears to have been the most successful in this sense, as opportunities for joint exploration of research data allowed new potential farming responses to the central question to emerge. The multi-stakeholder processes in the Australian case focused more on providing public openings for individual learning, and missed the opportunity for new knowledge to emerge through joint exploration. We conclude that participatory approaches may enable transformative practice through knowledge integration, but that this process is not an automatic outcome of increased community participation.