In 2012, Taiwan implemented a dual-track quality assurance system comprising accreditation and self-accreditation in higher education institutions. Self-accrediting institutions can accredit their programs without requiring approval from external quality assurance agencies. In contrast to other countries, the Ministry of Education of Taiwan authorized self-accrediting institutions to develop their own evaluation standards. This study investigated the institution-based accreditation standards and their implications on institutional internal quality assurance. Content analysis revealed that 37% of the indicators of self-accreditation were new and not used as review indicators in the original accreditation track. Two frequently added indicators were featured indicators and levels of internationalization. The results also indicated that institutions tend to structure their internal quality assurance systems uniquely. Three types of approaches for developing institution-based standards were identified: bottom-up, hybrid, and innovative approaches. Self-accreditation has benefited institutions committed to educational quality and pursuing excellence by enabling them to employ a fitness-for-purpose approach. The diversity of higher education and educational policy changes constitute new challenges to higher education. Balancing between accountability and autonomy is critical for all stakeholders of higher education.