PurposeThis study aims to examine the moderating effect of internal control on the relationship between internal quality assurance implementation and higher education institution (HEI) quality.Design/methodology/approachThe study employed a survey method with hypothesis testing using partial least squares-structural equation modelling (PLS-SEM) technique with a second-order analysis approach. The questionnaire survey was administered to 191 HEIs.FindingsThe results revealed that internal control and internal quality assurance implementations are positively associated with HEI quality. Additionally, internal control implementation strengthened the relationship between internal quality assurance and HEI quality.Originality/valueThis study adds to the body of knowledge on the moderating role of internal control in the HEI sector and its role in the non-economic aspect, namely, the HEI quality.