The article describes a process of preparing a research design on place-shaping, as outcome of a process of co-design between academic actors and non-academic actors in Brazil, South Africa and The Netherlands, taking place in the context of the project TRANSPLACE. The joint research design addresses varied sustainability issues as well as common challenges across areas of environmental change, in nine specific social-ecological settings in these countries. Key is the identification of innovative place-shaping practices or 'seeds of change', embedded in social-ecological systems and place-based assets. These seeds of change offer insight into how to support a place based approach to development, via the engagement and collaboration of varied actors. The article first reviews the literature on place and transformation. Furthermore the process of co-designing a joint research agenda is described. This process resulted in varied outcomes, such as a joint research agenda, the identification of 'seeds of change', and an overview of sustainability issues, learning challenges and involved stakeholders in the nine research sites. The article shows how engagement and learning in knowledge networks can be supported on different scales, and ends with lessons learned and perceived benefits of having gone through a co-design process.