Ethnobiology, defined as the scientific study of dynamic relationships among peoples, biota, and environments (SoE, 2017), is a field that combines different approaches from other disciplines while also including issues related to environmental and cultural ethics in order to understand and properly represent the complexity of relationships between cultures and their environments. Engaging in close collaboration with indigenous peoples from two societies in the Latin American tropics, and responding to national, regional and international legal and ethical guidelines, the aim of this study is twofold: (1) to propose a structured approach to first, engage with indigenous communities in formats locally relevant and accepted (i.e. following traditional and customary procedures and norms) while also ethically appropriate (i.e. following relevant codes of ethics and policy). (2) to engage in truly collaborative academic research, implementing a cross-paradigm process combining components of the collaborative ethnography and indigenous epistemologies. In order to demonstrate the effectiveness of these proposed procedures this study implements two ethnobiological researches, the first one on the effects of firearms introduction to the traditional hunting and fishing practices of the Tsimane' in Bolivia, and the second one on the importance of plants and associated knowledge (ethnobotany) in the process of fabrication and use of traditional bows and arrows. This second study has two components, a traditional ethnographic documentation of the information, and the production of a collaborative ethnographic film as a visual documentation and part of an applied representation of the results. All results (academic and applied) mutually complement and support one another, thus providing a holistic and more complete set of results. This study demonstrates that following ethical standards combined with local and customary regulations along with true collaboration, ethnobiological research can be a novel and innovative way to conduct research that benefits everyone involved producing locally relevant and academically significant results.