Conscience in the Age of Algorithms: Ethical Dilemmas in Generative AI Use Across Faith-Based Higher Education Institutions

This study explored the ethical tensions and dilemmas emerging across stakeholder groups- research administrators, faculty, and undergraduate students- regarding the use of Generative AI in academic research within faith-based higher education institutions in Mindanao, Philippines. A qualitative, holistic multiple-case study design was employed across five institutions, with fifteen participants (one administrator, one faculty member, and one student per institution) selected through purposive maximum variation sampling; semi-structured interviews were analyzed using reflexive thematic analysis for within-case analysis and Merriam’s five-step approach for cross-case synthesis. Nine essential themes emerged, three per stakeholder group, reflecting dilemmas of efficiency versus authentic learning, detection versus procedural fairness, innovation versus institutional integrity, assistance versus intellectual dependency, accuracy versus fabrication, professional judgment versus consistency, convenience versus genuine learning, confidence versus guilt and fear, and reliable detection versus equitable access to support, with institutional capacity emerging as a significant mediating factor that shaped both policy formalization and enforcement consistency. In addressing a contextual gap left by secular-focused studies, this research also fills a methodological gap: prior Philippine studies on faith-based AI governance relied largely on document analysis, whereas this study uses semi-structured interviews across three stakeholder groups within each institution, capturing lived experiences of ethical decision-making. The findings provide empirical evidence of how faith-based Philippine institutions navigate Gen AI ethical dilemmas and inform institutional policy design, faculty development, reform of detection practices, and student support mechanisms, particularly in resource-limited settings where ethical governance must be adapted to available capacity.