Indigenous food systems are particularly vulnerable to global shocks such as climate change, biodiversity loss, conflicts, pandemics and socio-economic crises. Agroecology, as a principle-based science, practice and social movement has a strong potential to make these systems more resilient. Nevertheless, a major challenge is to upscale agroecology beyond isolated successful examples. The recognition and demarcation of “indigenous lands” with focus on commons and on the preservation of local knowledge and culture is a potential opportunity to up-scale agroecology and improve the resilience of indigenous food systems. This study examines how indigenous territories and agroecology connect to each other in practice. We rely on a systematic review at global scale, a network analysis at national scale and a case study in the Bolivian Andes to look at the synergies and discrepancies that connect indigenous territories and agroecology. We found out that despite a high synergy potential, indigenous land rights and agroecology tend to be advocated for by separate networks. Furthermore, agroecological principles that focus on transition from high-input to more diversified agriculture are also ill-suited to the context of indigenous agriculture. Based on these findings, we propose pathways on how to harness the synergies between the consolidation of indigenous territories and agroecology.