At present, government-led research and other scientific institutions continue to face challenges in meaningfully weaving Indigenous Knowledge in research, thereby reinforcing the inequalities and exclusion faced by Indigenous Peoples. We found that, among other reasons, these challenges stem in part from a lack of tools and resources to guide researchers in engaging Indigenous partners ethically and respectfully throughout the research design, practice, and reporting phases, rather than to a lack of awareness or motivation. In response to this need, we developed an Inclusive Science Self-assessment Tool (ISSAT), an online questionnaire-based toolkit designed to support weaving Indigenous Knowledge Systems (IKS) in scientific research. ISSAT was developed for IKS through a three-year process that combined evidence synthesis with dynamic Indigenous rights-holder and stakeholder engagement. The evidence synthesis comprised a systematic review of ten years of relevant literature and a case analysis of how 215 federal scientists weave IKS in their research. Through the dynamic stakeholder approach, we engaged a cross-section of participants and experts across government, academia, and civil society whose input informed the development and validation of the tool. ISSAT users complete the questionnaire and receive tailored feedback with practical strategies for fostering inclusivity in scientific research, prompting self-reflection through an inclusive and relational research ethics lens. At the institutional level, the tool enables institutions to identify areas of need and prioritize limited resources to drive the institutional change needed for an inclusive, equitable, and diverse scientific enterprise.