Transdisciplinary education on sustainability for health has been primarily developed in high-income countries, yet the need in countries with limited research and human resource investments remains urgent. Little empiric documentation of the facilitators and barriers to transdisciplinary learning in such countries has been described. We assessed transdisciplinary learning among students of different disciplines collaborating with an Ecuadorian sustainability for health research project. Six undergraduate students from four different disciplinary backgrounds were incorporated through work-study agreements with provincial university academic supervisors. Learning was fostered and monitored through participant observations by a field supervisor. Students' learning was evaluated through subsequent in-depth interviews and visualization methods. Academic supervisor key informant and co-investigator observations aided triangulation. Qualitative data were analyzed using indicators of transdisciplinary thinking. Principal factors facilitating transdisciplinary learning were interaction with social actors, the integration of work with other disciplines, the use of alternative research techniques and methods, and the constant support of the field supervisor. Inhibiting factors included the existence of rigid academic rules, lack of training of the academic supervisors in diverse research methods, and social pressures to implement unidisciplinary foci. At the end of their link with the project, students had developed both cognitive outcomes and attitudinal values relevant to sustainable development for health. In countries with limited investments in research and human resources development, transdisciplinary approaches with social actors and engaged researchers can sensitize new professionals training in traditional academic contexts to the ecological-social-health problems faced by poor majorities and encourage their subsequent work on sustainability for human health.