The institution has an Internal Quality Assurance Cell (IQAC) responsible for monitoring and maintaining the standard of academic affairs. Chaired by the Principal, the IQAC's activities are planned, executed, and coordinated by an IQAC Coordinator with the assistance of faculty representatives from each domain.

At St Alphonsa College of Arts & Science, the IQAC performs regular tasks such as improving the quality of teaching and research based on student feedback, providing best practice inputs for efficient resource utilization and better services, and conducting academic and administrative audits to identify and improve weak areas. Feedback and suggestions from students and staff are collected through a Suggestion Box in the College Office or via email to the IQAC Coordinator at iqac@stalphonsa.edu.in.

The major activities of the IQAC include conducting academic audits, documenting annual staff and student feedback reports, planning and executing quality assurance measures in academic and curricular aspects, providing data for the monthly newsletter, documenting minutes of IQAC meetings, organizing seminars and workshops related to quality assurance, documenting all academic and outreach program activities, preparing reports for the National Accreditation and Assessment Council (NAAC), and preparing periodic reports for the Principal. Additionally, the IQAC documents self-appraisal reports of faculty members.