This article examines a holistic approach to science education by integrating scientific methodology with Indigenous knowledge systems and religious perspectives. Using examples from Qur’anic embryology descriptions and traditional ecological indicators employed by Indigenous communities for water‑quality assessment, the study demonstrates how non‑scientific epistemologies can complement, enrich, and sometimes precede modern scientific findings. The paper argues that adopting a holistic framework—combining reductionist scientific analysis with systems thinking and culturally grounded ways of knowing—can broaden learners’ perspectives and strengthen critical reasoning. This approach is increasingly relevant in an AI‑shaped educational landscape where students encounter diverse sources of information. The article highlights the need for culturally sensitive, inclusive, and interdisciplinary science education that prepares learners to navigate complex global challenges.