The implementation of access and benefit-sharing (ABS) protocols, and especially the Nagoya Protocol, has created new hurdles for international collaborations around Indigenous Traditional Knowledge. Overall, these frameworks push for the development of novel collaborative North–South agendas to improve the fair distribution of benefits. The Green Health Project (Guatemala) aims to implement a culturally pertinent and mutually accepted framework for sustainable use, as well as ABS of traditional medicinal plants. It involves developing a consensus among Indigenous groups, government officials, industry, and academia. We describe steps undertaken to design and implement an intercultural transdisciplinary process that promotes trust building and advances herbal medicine research in a respectful and innovative way. This involves joint definition of goals and methods. The consortium co-researched Q’eqchi’ Maya traditional medicine, collected voucher specimens of medicinal plants with traditional Healers, identified their taxa, and later developed a literature-based evaluation identifying species for potential product development. No samples for further research and development were collected. By applying the emic–etic concept, the project helped improve understanding of the main drivers of each stakeholder and the associated obstacles for reaching an ABS agreement. The project also explored the emergence of potential new drivers for developing evidence-based herbal medicine from the perspectives of academia, policy, cooperation, and grassroots Indigenous movements.