The study aims to investigate the implementation of the internal quality assurance system (IQAS) on HEIs performance, mediated by financial management accountability. The commitment from foundation leadership on financial management accountability and their implications for HEIs’ performance is also carefully examined. This study employs samples of 108 respondents from the leadership of private HEIs under Region IV Service Institutions. The purposive sampling, as a part of non-probability sampling was chosen as the sampling technique. Statistical data analysis conducted by use the structural equation model to test the hypothesis. The results reveal that the implementation of IQAS does not influence the financial management accountability, but it has an essential role on HEIs’ performance. Moreover, foundation leadership’s commitment has a significant positive effect on financial management accountability and HEIs’ performance. Financial management accountability also has a significant positive effect on HEIs’ performance. Financial management becomes important because the entire activities of HEIs should end with financial reporting. Therefore, financial and non-financial aspects are two interrelated and complementary aspects in the accreditation process. The findings of this study suggest that that performance measurement is very crucial as a part of the efforts to meet the general accountability requirement for organizations, particularly in HEIs.