Value-based higher education institutions face dual legitimacy pressures to maintain distinctive normative identities while demonstrating academic credibility. Within science education, however, the quality of values integration—beyond its symbolic presence—remains underexamined. This study examined (1) differences between symbolic and epistemic dimensions of Islamic values integration, (2) their structural associations with instructional practices, and (3) cross-institutional consistency in these patterns. Using a cross-sectional multi-source design, data were collected from 150 biology education students, 10 course syllabi, and five instructors across four Islamic higher education institutions in Indonesia. Nonparametric analyses indicated that Islamic values were highly visible in instructional practices, whereas engagement with scientific epistemic practices received substantially less emphasis, resulting in a large, statistically significant difference. Strong positive associations among instructional dimensions indicated that planning and assessment practices were structurally interconnected with opportunities for epistemic engagement. These patterns were consistent across institutions, suggesting systemic rather than institution-specific dynamics. Conceptually, the findings position values integration along a continuum from symbolic visibility to epistemic depth, indicating that current practices operate predominantly at the symbolic level. This study offers an empirically grounded analytical framework for evaluating the quality of values integration in value-based science education contexts.

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