PurposeThis study investigates internal control implementation contribution to quality management at higher education institutions (HEIs).Design/methodology/approachThis study employed a qualitative method by conducting semi-structured interviews. The research respondents (interviewees) consisted of internal auditors, HEI management members and accreditation assessors of Indonesian HEIs. A total of 15 respondents were successfully interviewed to collect the data; 12 were from different HEIs, and 3 were from the HEI accreditation board.FindingsThis study deduced that internal control implementation could contribute to HEI quality management and improvement if integrated with other control policies, such as internal quality assurance, performance measurement systems and performance-based budgeting. By doing so, internal control corroborates total quality management (TQM) implementation within HEIs since it promotes employee empowerment and supervision, reduces budget wastage, increases the achievement of budget targets on output and outcome of programs and activities, enhances strategic and integrated system practices, provides reliable information for better decision-making, and promotes effective communication and coordination and good leadership culture.Practical implicationsThe current study presents beneficial suggestions for HEI management on how internal control contributes to quality management at HEIs.Originality/valueAs suggested by Chalmers et al. (2019), most studies related to internal control were conducted in profit-oriented organisation settings, i.e. companies, and focused on their impact on economic aspects, such as profitability, cost efficiency and fraud mitigation. Meanwhile, internal control-related studies in the context of non-profit-oriented organisations, such as HEIs, and their role in non-economic aspects, in this case, the quality management in HEIs, is still lacking.