Indigenous Knowledge, Practice, and Belief Systems (IKPBS) are an ecological and cultural framework with which Indigenous communities have (and continue to) adaptively manage their land since time immemorial. In the current context of climate change and colonial forest and fire management in the western US, Indigenously‐led ecological research and cultural revitalization offers a path forward where tribal sovereignty of land stewardship is maintained and the resiliency of natural systems are reestablished. We describe our process of developing an Indigenous‐Directed Research (IDR) partnership to study xánthiip (Karuk for black oak, Quercus kelloggii), a Karuk cultural focal species, in the context of Karuk‐led forest restoration. We first outline our process of IDR by describing how this partnership was established, research questions and methodologies were co‐developed, IKPBS were centered, and utility to tribal forest restoration processes were prioritized. The primary product of this partnership was a culturally responsive black oak monitoring protocol to assess black oak tree quality over time. We describe how this protocol was developed including conducting semi‐structured qualitative interviews with Karuk cultural practitioners, translating qualitative interviews to field protocol metrics, consulting with research partners, testing for field feasibility, and sharing back to the local community through field training and youth curriculum development. Second, we analyzed plot data collected from the implementation of the black oak protocol using a two‐eyed seeing approach that ensured our ecological findings had cultural relevance for future Karuk‐led forest stewardship. Through this analysis we described the dominant black oak tree typologies based on their traits of importance as identified by Karuk cultural practitioners and research collaborators. All natural resources research takes place on Indigenous land. By outlining the steps of this transdisciplinary IDR partnership, we provide a framework for centering IKPBS, respecting Indigenous land sovereignty, and centering Indigenous leadership in ecological research and knowledge co‐development.