Despite the increasing demand to develop cross-disciplinary research projects, designing collaborative research still prove to be difficult due to both scientific specialization and organizational issues. In this paper, we explore how innovative design dynamics can be developed between researchers to collectively build research projects that could become common purposes for collaboration. This work relies on a case study led with the newly formed Eco&Phy research team, who applied an innovative design process to initiate collaboration and design its scientific agenda for the next 5 years. This process was built based on both KCP and matching-building methodologies: it included an initialization phase, during which the team strategically chose topics to be explored, and exploration phases, during which researchers collectively developed new knowledge and concepts to build cross-disciplinary projects. At the end of the design process, the team had developed two new research lines that were integrated in its official agenda. In conclusion, the article discusses the relevance of design approaches to develop original collaborative research through dedicated innovation processes.