Background: Detailed qualitative information regarding Indigenous populations’ health-seeking behaviours within Peru’s plural healthcare system is lacking. Such context-specific information is prerequisite to developing evidence-based health policies and programs intended to improve health outcomes for Indigenous populations. To this end, this study aimed to characterize health-seeking behaviours, factors affecting health-seeking behaviours, and barriers to obtaining healthcare in two Indigenous Shawi communities in Peru. Methods: Community-based approaches guided this work, and included 40 semi-structured interviews and a series of informal interviews. Data were analysed thematically, using a constant comparative method; result authenticity and validity were ensured via team debriefing, member checking, and community validation. Results: Shawi health-seeking behaviours were plural, dynamic, and informed by several factors, including illness type, perceived aetiology, perceived severity, and treatment characteristics. Traditional remedies were preferred over professional biomedical healthcare; however, the two systems were viewed as complementary, and professional biomedical healthcare was sought for illnesses for which no traditional remedies existed. Barriers impeding healthcare use included distance to healthcare facilities, costs, language barriers, and cultural insensitivity amongst professional biomedical practitioners. Nevertheless, these barriers were considered within a complex decision-making process, and could be overridden by certain factors including perceived quality or effectiveness of care. Conclusions: These findings emphasize the importance of acknowledging and considering Indigenous culture and beliefs, as well as the existing traditional medical system, within the professional healthcare system. Cultural competency training and formally integrating traditional healthcare into the official healthcare system are promising strategies to increase healthcare service use, and therefore health outcomes.