There is currently a resurgent interest in traditional medicine. The World Health Organization suggested applying strategies for its proper integration into the National Health System. This study seeks to know and understand the opportunities and challenges of the practice of Andean traditional medicine (ATM) in Cuenca (Ecuador) within the context of a possible integration with modern medicine (MM) from the perspective of healers, physicians, and users. The study is qualitative and has a phenomenological design. Convenience and snowball sampling was applied to select participants for focus groups, individual semi-structured interviews, and individual non-participatory observations. The information was qualitatively processed, and the findings categorized into 2 major themes (a. Opportunities in the practice of ATM, and b. Challenges in the potential integration of ATM in MM) and 14 associated subthemes, respectively 6 in the first main theme and 8 in the second main theme. Participants characterized the strengths and weaknesses in integrating Andean traditional medicine with modern medicine. Findings suggest that an appropriate integration of ATM with MM request a government regulatory framework encouraging the protection of ancestral wisdom and biodiversity, a safe and rational application of joint therapies, and research development in the area.