This analysis presents methodological innovations and co-design lessons emerging from a Transdisciplinary Participatory Research Program conducted between 2018 and 2025 in the Upper Madera River Basin, a complex socio-ecological frontier between Bolivia and Brazil. The study integrates two complementary initiatives: the Transdisciplinary Participatory Research on Governance and Infrastructure (2018–2022), developed under the Governance and Infrastructure in the Amazon (GIA) project, and the Transdisciplinary Participatory Research Program in the Bolivian Amazon (2023–2025). Together, these efforts brought community researchers, Amazonian university students, scholars from Bolivia, Brazil, and the United States, and practitioners into collaborative processes addressing fisheries, agroforestry systems, sustainable tourism, forest degradation, and local livelihoods. Methodologically, the program advanced an innovative hybrid model combining participatory fieldwork, local ecological knowledge, hydrological modeling, participatory mapping, and ethnography. These approaches fostered a dialogue of knowledges, promoting shared responsibility in knowledge production and enabling a situated understanding of environmental change and infrastructure impacts. Rural and urban communities—key actors in territorial governance—played a central role by validating methods, setting priorities, and strengthening local decision-making. A structured mentoring system linking local universities, international mentors, expert institutions, and community organizations enhanced research capacity and experiential learning. Students became junior researchers and territorial stewards, developing skills in participatory methodologies, environmental monitoring, communication, and research ethics. Despite challenges such as administrative delays, unequal access to resources, and misaligned academic and community timelines, the program demonstrated how transdisciplinary research can foster local autonomy, intercultural dialogue, and democratic knowledge production. It also underscores the need for Amazonian universities to adopt clear strategies that support interdisciplinary programs with meaningful territorial impact. Keywords: Transdisciplinary Research, Participatory Knowledge Co-Production, Amazonia, Diálogo de Saberes (Dialogue of Knowledges), and Environmental Governance.