HEEACT conducted the First Cycle of Program Accreditation from 2006 to 2010, evaluating a total of 1,907 programs from 79 institutions. Following that, HEEACT initiated the Evaluation of General Education and the Second Cycle of Program Accreditation, which took place from 2012 to 2016. In the second cycle, 11,847 programs from 83 institutions were evaluated.

 In 2017, the Ministry of Education (MOE) introduced a significant policy change, making Program Accreditations voluntary instead of compulsory. Consequently, institutions were given the autonomy to decide whether to undergo external quality assurance (EQA) and choose the accrediting agency. As a government-funded national QA agency, HEEACT continues to offer quality assurance services, accepting commissions from domestic institutions to conduct Program Accreditation.

 The QA standards were developed based on the philosophy that programs should recognize their unique academic position and foster a culture of quality assurance. By reviewing the practices and experiences of accrediting organizations in Taiwan and abroad, these standards were combined with the plan-do-check-act (PDCA) management method. This approach helps programs assess their practices and outcomes based on three major standards: (1) Program Development, Governance, and Improvement; (2) faculty and teaching; and (3) students and learning.