The purpose of this study was to examine methods used to document and protect indigenous health knowledge among traditional medical health practitioners (TMHPs) in Kenya and to strengthen its sustainable management. The objectives were to: determine methods used by TMHPs to protect and document traditional indigenous health knowledge; assess the effectiveness of existing protocols in protecting and documenting traditional health knowledge; examine challenges faced by TMHPs in protecting and documenting traditional health knowledge and suggest effective strategies for protecting and documenting traditional health knowledge. Guided by the SECI model and Social Exchange Theory, this qualitative case study involved 30 traditional medical registered practitioners and 7 key informants. Data was collected through interviews and observations and analyzed thematically. The findings reveal that documentation is largely informal, oral and practitioner-controlled, while protection relies on secrecy and restricted sharing within trusted networks due to fears of exploitation and loss of ownership. Documentation remained largely informal, oral, and practitioner-controlled, while protection relied on secrecy, custodianship, and restricted sharing owing to concerns about misuse, loss of ownership and livelihood security. Existing documentation and protection mechanisms were perceived as ineffective because formal documentation and protection systems remained poorly aligned with indigenous practices and were weakly implemented. The study concludes that the protection of indigenous health knowledge is severely hindered by this systemic misalignment between formal frameworks and traditional practices. To address these gaps, the study recommends developing hybrid documentation systems that integrate formal protection mechanisms with indigenous knowledge structures to ensure both preservation and livelihood security.