Biodesign is an emerging disciplinary field that, in its multifaceted nature, finds in transdisciplinarity a promising pathway to address the complex challenges posed by contemporary scenarios. However, specific methodologies that connect the design mindset with the epistemological framework of scientific methods are still lacking. How can we grow the next generation of biodesigners in this scenario? Transdisciplinary dialogue provides a foundation for merging design thinking with scientific reasoning, leading to the development of methodologies and educational strategies aimed at creating shared languages and codes that promote synergy between design and science. This study presents the results of a methodological evolution—from multi and interdisciplinary approaches to transdisciplinary ones—through a workshop focused on material design, a course designed to train future biodesigners. This workshop engaged students in collaborative material tinkering activities, working side by side with scientists in an active laboratory setting. The study demonstrates that combining a material-driven design approach with scientific methodologies fosters iterative dialogical relationships, ultimately enriching and substantiating the final design outcomes.