This study examined the integration of Indigenous Knowledge Systems (IKS) into educational leadership practices and their impact on school governance and decision-making in public secondary schools in Cross River State, Nigeria. It also explored the role of legal recognition and policy support in facilitating IKS integration and the contribution of principals to culturally responsive and community-based education. A descriptive survey design was employed, targeting all 325 principals in public secondary schools. Data were collected via a structured four-point Likert scale questionnaire and analyzed using Chi-square tests. Findings revealed a significant association between IKS integration and educational leadership practices (χ² = 15.72, df = 6, p = 0.015), indicating that principals who actively incorporate indigenous knowledge enhance culturally relevant leadership and school governance. Legal recognition and policy support were significantly linked to IKS integration (χ² = 18.46, df = 6, p = 0.005), emphasizing the role of formal frameworks in sustaining indigenous knowledge. Additionally, principals’ leadership practices significantly influenced the promotion of culturally responsive and community-based education (χ² = 14.89, df = 6, p = 0.022), demonstrating that active engagement with community traditions strengthens educational relevance and inclusivity. The study recommends institutionalizing IKS through policy support and encourages principals to continue fostering community-based practices to improve educational outcomes and cultural preservation in Cross River State.