Emphasizing the principles of good governance and Corporate Social Responsibility (CSR), the study underscores the importance of instruments promoting responsible inclusion of stakeholders in academic decision-making. This paper delves into the intricate landscape of university governance, focusing on aligning mechanisms within Higher Education Institutions (HEIs). We navigate through the complexities of governance, emphasizing diverse stakeholder involvement crucial for effective decision-making in the unique context of universities. Applying the lens of agency theory, we explore relationships between principals and agents, highlighting challenges arising from divergent interests and information asymmetry. The study advocates for further research on governance, emphasizing perspectives of the governed and marginalized. Methodologically, our research design incorporates a conceptual framework from expert workshops, a structured questionnaire to a diverse student population, and advanced analysis techniques. Results reveal key components—teacher compliance, student compliance, student difficulties, and external activities—shedding light on factors influencing student satisfaction with virtual education. In conclusion, this paper provides comprehensive insights into aligning mechanisms in university governance, particularly within virtual education platforms. Contributions extend to governance, agency theory, and the challenges and opportunities presented by virtual education. Findings hold implications for institutional decision-makers, educators, and policymakers seeking to enhance governance processes and improve the quality of virtual education in higher education institutions.