Climate change impacts global food systems and while attention has shifted to solutions within some sectors, there is a need to engage in meaningful collaborations across all disciplines. Globally, Indigenous communities care for and protect a significant portion of the world’s biodiversity despite only representing 6% of the global population. This emphasizes the significant role that Indigenous knowledges and traditional ecological knowledge (TEK) have in protecting the earth and supporting collective food systems. Therefore, Six Nations Polytechnic, a post-secondary and Haudenosaunee-led school located at Six Nations of the Grand River in Ohsweken, Ontario, Canada, is collaborating with community partners and local Universities to create pathways for TEK education. Six Nations and surrounding Haudenosaunee communities have identified a need to support youth and future leaders in environmental science training that is grounded in cultural knowledge and methodologies. Current STEM programs are often in contrast to Indigenous perspectives, creating barriers to Indigenous youth in pursuing these educational pathways; however, Indigenous communities are disproportionately impacted by climate change. Through the leadership of Haudenosaunee scholars, Knowledge Holders, and researchers, including engineers, hydrologists, anthropologists, and health and nutrition scientists, our team has begun co-creating micro-credential courses, a STEM camp with a university course credit, and diploma programs that address community and ecological needs for sustainability. These courses are informed by Six Nations youth and university students’ feedback. A major theme within this work is the intersection of knowledge to ensure sustainable food systems for Indigenous communities and beyond. Based on the TEK course development to date, we make policy recommendations to strengthen Indigenous led food sovereignty education and research that have valuable implications for interdisciplinary food systems education.