Purpose: This paper aims to present the lessons learned during the design and implementation of a quality assurance system (QAS) in an academic unit and considers the regulatory changes to institutional accreditation in Chilean higher education, the international standard ISO 21001:2018, and the stakeholders' requirements. Design/methodology/approach: This study uses an abductive approach to identify and evaluate the key factors to implementing a QAS in higher education institutions (HEI). Qualitative and quantitative data were collected through questionnaires, semistructured interviews, focus groups with stakeholders, a literature review and official institutional documents. Documents and interviews were subjected to content analysis using a process of inductive coding to identify and define topics or categories. A descriptive statistical analysis of categorical variables calculated the marginal frequency of each response. All information aided in designing the QAS for the school and its implementation plan. Findings: This study highlights major challenges universities could face while implementing QAS, illuminating key principles and reflecting relevant practices. The lessons learned in this process show the importance of balancing accountability and continuous improvement while promoting a more receptive organizational culture, aligning the national and international standards in the early design stage, understanding the roles and responsibilities of the staff, having the support of a quality office and performing a gap analysis. Originality/value: This work provides other HEI in need of designing and implementing a QAS with a conceptual and solid framework to integrate internal, external and international regulations of quality assurance criteria and standards. This paper could become a valuable reference for university managers, practitioners and quality professionals facing similar challenges.