The mushrooming of private and public universities in Kenya as well as pressure from a rapidly transforming labour market has given rise to new concerns about quality in higher education. One of the ways in which universities assure quality and acquire recognition in their home countries and abroad is through accreditation and certification. In addition, universities seek quality certification so as to differentiate themselves from the many institutions that are offering degrees and diplomas which have become commodities in the market economy. Despite being ISO 9001:2008 Certified, previous audit reports indicate various non-conformities across various systems of Moi University. The study therefore sought to investigate systemic barriers to ISO compliance in Moi University. This paper, derived from the study, explores the inta-sectional, inter-sectional, intra-departmental, inter-departmental, inter-school and inter-campus barriers to ISO compliance. The study was both qualitative and quantitative in nature. Data were collected by means of semi structured questionnaires supplemented by interview schedule guides. The target population for the study was 1,343 officers drawn from the various systems of the institution. Stratified random and purposive sampling techniques were employed in selecting respondents. The sample size was computed as 404 officers who constituted 30% of the target population. This included top management, Directors, Deans, Heads of Department, lecturers and administrative staff. Cumulative frequencies, percentages means and standard deviation were computed to help derive meaning from quantitative data. Qualitative data from interview schedule guide were transcribed, thematically classified and arranged before being reported in narrations and quotations. Findings were presented in form of tables, charts and graphs. The study established that there are barriers within sections, departments, schools and campuses hindering the effective implementation of ISO 9001:2008 standards. It was therefore recommended that since top management leadership is the backbone of implementing ISO 9001:2008 standards, the top management should be fully committed towards the improvement of services at the University.